This is a static version of the conservation advice for this site, generated on 20/09/2019.
Please check the latest advice for this site at
Natural England Conservation Advice for Marine Protected Areas
Isles of Scilly Complex SAC

Natural England guidance

This site collection contains Natural England's conservation advice for this site. It fulfils Natural England’s responsibility under the Conservation of Habitats and Species Regulations 2017 (as amended), to give advice on how to further the conservation objectives for the site, identify the activities that are capable of affecting the qualifying features and the processes which they are dependent upon.

Natural England's conservation advice for this site is made up of a number of components. You will need to consider: Additional information for consideration:

Site information

Overarching site: Isles of Scilly Complex SAC
Site name: Isles of Scilly Complex SAC
Designation type: SAC
Site identification: UK0013694
Latest designation date: 20 May 2004
Qualifying features
(click to see site specific description):

Grey seal (Halichoerus grypus)

Grey seals are present in the Isles of Scilly SAC throughout the year, including a well-established breeding population. About 40% of the world’s grey seal population is found around the UK, with estimates of up to 1000 grey seals being based in the Isles of Scilly and Cornwall. The seals around Scilly belong to the Northeast Atlantic sub-population (Isles of Scilly Area of Outstanding Natural Beauty Partnership, 2014), (Bowen, 2016)

The grey seal population in Scilly appears to be relatively stable and is focused around the Northern, Eastern and Western Rocks (Sayer, 2012), (Sayer and Witt, 2018). Grey seals spend a large amount of time at sea, but access to suitable coastal haul-out sites is very important for resting, digesting food, moulting and pupping. The pupping season in the Isles of Scilly can extend from August until December (Sayer, 2012). The Scillonian population of grey Seals accounts for around 40% of pups born in the South-West region (Duck, 1996).

Grey seals from the Isles of Scilly are not a discrete population and mix with those on the mainland. Seals from the photo ID catalogue in Scilly have been identified in Cornwall, Brittany, Ireland and at Skomer in Wales (Isles of Scilly Area of Outstanding Natural Beauty Partnership, 2014), (Bowen, 2016).


Intertidal coarse sediment

Intertidal rock

Intertidal sand and muddy sand

Water column

Mudflats and sandflats not covered by seawater at low tide

The Isles of Scilly has extensive intertidal sandflats (no mudflats) sheltered between the islands. The sandflats exposed at low tide enjoy fully saline conditions, shelter from strong wave action and a variety of tidal currents. The sediments contain little mud due to the low suspended sediment in surrounding seas resulting from the islands’ isolation and the presence of oceanic water (Gilland and Crix, 1995). One of the largest sandflats in Scilly is St Martin's Flats, off the south west coast of St Martin's which is also designated as a Site of Special Scientific Interest (SSSI), St Martin's Sedimentary Shore SSSI. The intertidal sand here is formed from medium to coarse quartz sediments (Natural England (NE), 2010) derived from the granite that forms Scilly. The sandflats are moderately exposed, influenced by complex local tidal and current patterns, leading to sediment sorting, periodic reshaping and mixtures of habitat types and associated communities.


Intertidal sand and muddy sand

Intertidal sand communities in Scilly are species-rich, particularly those between the northern islands. This habitat supports communities of burrowing anemones, bivalves, terebellid worms and heart urchins, with species present which are normally restricted to the subtidal. This could be due to the archipelago’s granite nature, which means intertidal sediments are often medium to coarse grained (Natural England (NE), 2010) and more like those found offshore, in addition to the mild climate (Gilland and Crix, 1995). These normally subtidal species include the rosy feather-star Antedon bifida, the seven-armed sea star Luidia ciliaris and the European lancelet Branchiostoma lanceolatum (Natural England (NE), 2010). The heart urchin Echinocardium cordatum, purple heart urchin Spatangus purpureus and razor shells Ensis spp. are further species found which are usually subtidal. There are also southern species recorded from the sandflats which are rarely found on the mainland, including the hermit crab Cestopagarus timidus and the spiny cockle Acanthocardia aculeata (Brown et al., 1997).

One of the largest sandflats in Scilly is St Martin's Flats, off the south west coast of St Martin's which is also designated as a SSSI, St Martin's Sedimentary Shore SSSI. The community compositions here do not directly match biotope classifications. There are 3 distinct communities with characteristic species that typify assemblages present: the clam Dosinia exoleta , the worms Arenicola marina , and Scoloplos armiger , and the heart urchin Echinocardium cordatum , and Opheliid polychaetes (Natural England (NE), 2010).


The islands and rocky islets in Scilly are surrounded by reefs, some only extending into the shallow subtidal, others extending well beyond 50m depth. The location of the islands, exposed to the full force of the Atlantic, leads to the development of extremely exposed communities on the west facing reefs, whilst on the east facing coast, more sheltered and silted reefs occur.

The reef in Scilly is made up of the intertidal, infralittoral and circalittoral rock sub-features. Over 150 species of seaweed have been recorded from the intertidal and subtidal reefs of Scilly (Gall, 2011). The intertidal under-boulder communities occurs from the mid shore to the lower extreme shore (Selley et al., 2014). The orange peel bryozoan Turbicellepora magnicostata is only recorded in Scilly in the UK, and the nationally scarce cushion star Asterina phylactica is present (Selley et al., 2014). The infralittoral rock feature supports kelp forest communities, characterised by Laminaria hyperborean and Laminaria ochroleuca, with rich understorey communities of red algal species (Axelsson, 2014). The circalittoral rock feature includes upstanding reef and large boulders communities, including vertical rock communities supporting characterising and notable species including the jewel anemone Corynactis viridis, Devonshire cup coral Caryophyllia smithii, ross coral Pentapora fascialis, Plumose anemone Metridium senile, dead man's fingers Alcyonium digitatum, and spiny lobster Palinurus elephas (Eggleton and Meadows, 2013). Important and well-developed communities of erect and branching sponges and the pink sea fan Eunicella verrucosa have been recorded at a number of sites, mostly to the west of the islands. These communities are species rich and include mature fragile slow growing species which makes them of high conservation importance (Gall, 2011). Circalittoral low lying boulders and raised bedrock communities characterised by ross coral Pentapora fascialis and Devonshire cup coral Caryophyllia smithii are dominant in the offshore region to the north of the isles (Eggleton and Meadows, 2013).


Circalittoral rock

Circalittoral rock surrounds the archipelago, ranging from sheltered reefs to exposed and tide-swept reefs outside the shelter of the islands. Reefs in Scilly support diverse communities of anemones, sponges, anthozoans, red algae and hydroids, with fauna depending on their location (Irving and Northen, 2012) Commonly-found mobile species are the urchin Echinus esculentus and black sea cucumber Holothuria forskali (Axelsson, 2014).

Circalittoral rock in Scilly supports particularly rich sponge communities and the Priority Habitat ‘Fragile sponge and Anthozoan communities on subtidal rock habitats’ occurs (Lewis et al., 2008). This habitat is typically located on silty reefs below 22m, at sites with intermediate exposure and strong currents. These reefs are primarily found towards the south east and north east of the archipelago, outside the shelter of the main islands (Gall, 2011) (Lewis et al., 2008). More warmer water species are found in this Priority habitat in the Isles of Scilly than the rest of the UK, notably the sponge Endectyon delaubenfelsi (Goodwin and Picton, 2011). Rare species include the slime sponge Desmacidon fruticosum, branching sponge Adreus fasicularis and encrusting sponge Hexadella racovitzae while Antho granditoxa and Axinella flustra have not previously been recorded in the UK (Goodwin and Picton, 2011). Nationally scarce anthozoans on these reefs include include red sea fingers Alcyonium glomeratum, pink sea fingers Alcyonium hibernicum, white cluster anemone Parazoanthus anguicomus and the warted corklet anemone (Gall, 2011).

Vertical rock faces are present on reefs across the archipelago and typically dominated by the jewel anemone Corynactis viridis with the Devonshire cup coral Caryophyllia smithii, Dead man’s fingers Alcyonium digitatum, sponges and the spiny starfish Marthasterias glacialis all relatively abundant. (Seasearch, 2010)(Axelsson, 2014). Trenemene Reef in the Western Rocks supports jewel anemones, elegant anemones Sargartia elegans and plumose anemones Metridium senile on its vertical rock faces. The nationally scarce sea slug Doris sticta has also been recorded. Similar fauna were identified on vertical rock faces across the archipelago by Seasearch divers, from south of St Agnes to north of St Martins (Seasearch, 2010).

Infralittoral rock

High water clarity around the Isles of Scilly means that the infralittoral zone extends into deeper water than around the mainland, with kelp recorded at 30m (Barne et al., 1996). Cuvie Laminaria hyperborean and golden kelp Laminaria ochroleuca are the most prevalent kelp species in Scilly, with four other kelp species also found in the infralittoral zone (Axelsson, 2014). Cuvie is usually the canopy forming kelp species on the mainland, but golden kelp (a warmer water species) is commonly found on Scilly (Seasearch, 2010) and the ratio of these two kelp species in the canopy varies between sites. Golden kelp was found to dominate the canopy at survey locations in the south, west and north of the archipelago during surveying in 2013, whilst cuvie dominated in the east (Axelsson, 2014) presence and abundance of golden kelp is expected to increase as sea temperatures rise, and there is evidence that significant changes are already occurring (Smale et al., 2015). This is likely to affect kelp forest communities in Scilly.

A diverse range of red algal species have been identified in Scilly, with at least 50 recorded in the kelp understorey (Irving and Northen, 2012) Differences have been found in the species composition of red algal communities at sites depending on whether cuvie or golden kelp was the dominant canopy species. A wide range of faunal species inhabit the infralittoral zone; including encrusting sponges, anemones, starfish Asterias rubens and Marthasterias glacialis and sea cucumbers Holothuria forskali. Urchins Echinus esculentus are common grazers in the kelp. Kelp forests also provide an important habitat and nursery ground for fish and the Ballan wrasse Labrus bergylta uses the kelp forests in Scilly (Axelsson, 2014).

Intertidal rock

Intertidal rock in Scilly supports a diverse range of species, with exposed shores tending to be animal-dominated and sheltered shores dominated by brown algae (Lewis et al., 2008). Species include some which are rare or never recorded on the mainland, like the encrusting bryozoan Turbicellepora magnicostata and others usually restricted to the subtidal, such as the featherstar Antedon bifida (Selley et al., 2014)(Gall, 2011). There are other noticeable differences in species composition from communities on the mainland, with species such as the brown seaweed Bifurcaria bifurcata and the glaucous pimplet anemone Anthopleura ballii more common, and species such as the barnacle Semibalanus balanoides nearly absent (Selley et al., 2014).

The Priority habitat ‘Intertidal Underboulder Communities’ is present in Scilly. These underboulder communities are again slightly different from similar communities on the mainland, with thongweed Himanthalia elongata typically dominating the canopy, instead of serrated wrack Fucus serratus. Underneath the canopy is a red algal understorey and the communities support a diverse range of fauna, including anemones, sponges, crabs, starfish and bryozoans. At least three species of stalked jellyfish are found in Scilly Haliclystus species, Calvadosia cruxmelitensis and Calvadosia campanulata and all are UK Priority species for conservation (Selley et al., 2014).

Nationally rare giant gobies Gobius cobitis are found in rockpools within the intertidal rock feature. Intertidal species present on Scilly which are nationally scarce include the scarlet and gold star coral Balanophyllia regia and the cushion star Asterina phylactica (Gall, 2011). There is a high diversity of seaweeds of significant conservation value on the shores of the Isles of Scilly (Gall, 2011)

Sandbanks which are slightly covered by sea water all the time

The Isles of Scilly archipelago, off the south-west tip of England, encompasses extensive sublittoral sandy sediments, which, between the islands, are contiguous with the intertidal sandflats. They are important in the UK for the extent and diversity of their associated communities (Joint Nature Conservation Committee (JNCC), 2018) and the site is considered to be one of the best areas in the UK for subtidal sandbanks. In particular, their isolation and the presence of oceanic water contribute to the special nature of the site, which is characterised by shallow sandy sediments with low silt content and by the fully marine salinity (Joint Nature Conservation Committee (JNCC), 2018).

The shallow sublittoral sediments are colonised by the most extensive and best-developed eelgrass Zostera marina beds in southern England (Brown et al., 1997). These beds have a rich associated flora and fauna of algae, hydroids, sea anemones, molluscs and fish. In addition, there are rich communities present on the tide-swept sandbanks in the narrow channels between the islands and in the deeper, more stable, wave-sheltered sediments. The fauna of these sediments includes tanaid crustaceans, a diversity of polychaete worms, and various echinoderms (Joint Nature Conservation Committee (JNCC), 2018). Tide-swept infralittoral cobbles and pebbles which may be highly mobile, create an environment that is difficult for many algae species to survive in. The Isles of Scilly have good examples of tide-swept channel communities of national importance (Lewis et al., 2008).

Several interesting species have been recorded in the subtidal sediments including the polychaete worm Spio mecznikowianus, the bivalve Bosemprella incarnata (Rostron, 1983) and the isopod Natatolana gallica (Rostron, 1989).


Subtidal coarse sediment

Subtidal coarse sediment forms a peripheral zone separating rockier areas from areas of extensive sand accumulation (Munro and Nunny, 1998) and has a varied distribution within the archipelago. Course sediments are also found and at greater depths, particularly within the southeast corner of the site (Munro and Nunny, 1998), (Eggleton and Meadows, 2013).

In these deeper areas, coarse sediments characterised by various polychaete worms, nematodes, bivalves and echinoderms can be found. For example, within the North West Channel to the south west of Samson at a depth of around 30m (Johnson et al., 2017).

In areas of high tidal flows, cobbles and pebbles can be support algal species. These communities are typical of tide swept channels and are of national importance (Lewis et al., 2008).

Subtidal mixed sediments

Small areas of subtidal mixed sediment can be found within the site, although the extent appears to be limited. Extensive grab sampling has only recorded mixed sediment west of Tean (Johnson et al., 2017). However, diver and drop video surveys suggest subtidal mixed sediment may be present in other areas (Marine Conservation Society (MCS), 2006), (Seasearch, 2009), (Isles of Scilly Wildlife Trust, 2009), (Isles of Scilly Wildlife Trust, 2010), (Oil Pollution Research Unit (OPRU), 1983), (Natural England and Cefas, 2011). These surveys recorded communities of Cerianthus lloydii and other burrowing anemones which are generally characteristic of circalittoral mixed muddy sediment.

Subtidal sand

Subtidal sand can be found in the channels between islands, in sheltered bays and at sheltered depths as well as in the more exposed areas of the site. Areas of mobile medium grained sand forming shoals of mega-ripples are common in shallower areas of strong tidal flow. For example, in the vicinity of Crow Bar, in St Mary’s Sound and in channels between the islands. Some of these areas are also likely to be regularly influenced by wave action.

In deeper and more sheltered areas, finer sands settle out. These sediments are more stable but may still be disturbed during storms. For example, off the North East Shore of St Mary’s in Crow Sound (Munro and Nunny, 1998).

Various small crustaceans, mobile and tube dwelling polychaete worms, echinoderms and bivalve molluscs can be found within the subtidal sand.

Subtidal seagrass beds

The Isles of Scilly archipelago encompasses a widespread area of shallow, submerged sandbanks which link individual islands providing an abundance of suitable habitat for seagrass (Marine Ecological Surveys Limited, 2017). The shallow sublittoral sediments are colonised by the most extensive and best developed Zostera marina beds in southern Britain (Brown et al., 1997). The seagrass beds in the Isles of Scilly are primarily subtidal, although they do extend into the intertidal in some areas (Lewis et al., 2008).

Seagrass beds were once abundant and widespread around the British coast, but serious declines have occurred in particular as a consequence of a severe outbreak of ‘wasting disease’ in the early 1930s. The recovery of eelgrass beds since the 1930s has been slow and patchy and this habitat is now considered nationally scarce in the UK. Large areas of seagrass were also lost in Scilly during this epidemic and the five main seagrass beds may have originally been one large bed. (Lewis et al., 2008).

There are two main areas of seagrass beds within the SAC. The first is a band of seagrass which runs from Samson and southwest of Tresco north towards Tean, and the second seagrass beds which surround the Eastern Isles (Marine Ecological Surveys Limited, 2017). Substantial beds are also found in St. Mary's Harbour and at Bar Point, St. Mary's, while smaller beds are found at Rushy Bay, Bryher, Tresco East at Old Grimsby Harbour and north of St. Martin's at Porth Morran (Marine Ecological Surveys Limited, 2017). A small seagrass bed was found at Samson in 2010 however no seagrass was recorded here in 2016 (Marine Ecological Surveys Limited, 2017), (Jackson et al., 2011).

The seagrass bed communities have an unusually rich associated biota including various seaweeds and fish, and rich sediment communities of anemones, polychaete worms, bivalve molluscs and burrowing echinoderms. Many southern species are present, often in large numbers, including some which are only rarely recorded in Britain (English Nature, 2000), (Munro and Nunny, 1998). Colonial diatoms are abundant on the leaves of the seagrass and a variety of filamentous brown algal epiphytes, encrusting coralline algae and other algae live on the seagrass.

Shore dock (Rumex rupestris)

Shore dock is a nationally rare species and the population in the Isles of Scilly marks the south-west extent of the plant’s English range. In the UK, shore dock is known to be found at 40 locations in South-West England and Wales. The total UK population is estimated to comprise less than 650 plants (Parslow, 1996).

Within the Isles of Scilly, historical records show shore dock used to be present on 7 of the larger islands and a number of rocky outcrops (Joint Nature Conservation Committee (JNCC), 2017). However, in recent years it is thought to have been present on only 4 of the islands in the archipelago; Annet, Tean, Samson and Tresco (Joint Nature Conservation Committee (JNCC), 2017). This species has been found on the boulder beaches of Annet and Tean, the foreshore and sandy dunes on Samson and at the south of end of Tresco (Natural England, Unknown).

Monitoring in autumn 2014 found winter storms destroyed shore dock populations on Annet, Tean and Samson, and the most recent surveys in 2017 found only 1 plant (on Tean), however Annet could not be visited during that survey.

General information on the site features:
The generic information on the qualifying features is useful for understanding the qualifying features, and should be used in conjunction with the site specific information.
Designated area (ha): 26849
Component Sites of Special Scientific Interest (SSSI):
Overlapping Protected Areas:

Last updated: 15th March 2019

Background information and geography

The Isles of Scilly are a granite archipelago situated approximately 28 miles off the south west coast of Cornwall, renowned for their pristine marine environment and diverse fauna. Due to the archipelago’s southerly location, lack of coastal influences and range of exposures, species assemblages here are different from the mainland UK. A range of warmer water species are noticeably more prevalent on Scilly (Barne et al., 1996). The Isles of Scilly Special Area of Conservation (SAC) encompasses all of the main islands and outlying rocky islets and protects a range of habitats. Rocky reefs in Scilly stretch from the intertidal to deep circalittoral reefs and are recognised for the diversity of species they support. These include corals, sponges, seaweeds and bryozoans. The nationally rare orange peel bryozoan Turbicellepora magnicostata is found on intertidal rock in the Isles of Scilly, but nowhere else in the UK (Selley et al., 2014). Priority species for conservation on the reefs include pink sea fans Eunicella verrucosa, sea fan anemones Amphianthus dohrnii and sunset cup corals Leptopsammia pruvoti (Gall, 2011) (Lewis et al., 2008).

Extensive intertidal sandflats are present in the shallow water between the islands and again support a wide range of species, including some not often found in the intertidal. The largest of these sandflats is found off the south-east coast of St Martins. These sandflats often extend into the subtidal, where they support extensive and well-studied Zostera marina seagrass beds, and diverse subtidal sediment communities.

In addition to habitats the Isles of Scilly SAC is designated for supporting a sizeable population of grey seals Halichoerus grypus, which are present all year round and shore dock Rumex rupestris on a number of the islands.

The Isles of Scilly SAC overlaps with 10 of the 11 more recently designated Marine Conservation Zones (MCZs). The MCZs complement the SAC designation by offering protection to species and habitats that are not protected by the SAC. These include specific intertidal rock and sediment habitats, spiny lobster Palinurus elephas and two species of stalked jellyfish Calvadosia campanulata and Haliclystus auricular. There is also an SPA in Scilly, designated for breeding seabirds.

Site maps

Use the MAGIC website to see site maps, including habitats, species and other marine designations.

These maps are based on best available evidence, there are some caveats associated with the maps on MAGIC.

There are some instances where the feature, subfeature or supporting habitat name varies on MAGIC from the conservation advice. The alternative names are listed on

The dynamic nature of habitat features and supporting habitats for mobile species is illustrated where data is available, as new evidence becomes available these maps will be updated with our current knowledge of their known extent.

Conservation objectives

The site’s conservation objectives apply to the site and the individual species and/or assemblage of species for which the site has been classified (the "Qualifying features" listed above).

The objectives are to ensure that, subject to natural change, the integrity of the site is maintained or restored as appropriate, and that the site contributes to achieving the Favourable Conservation Status of its qualifying features, by maintaining or restoring:
  • the extent and distribution of qualifying natural habitats and habitats of the qualifying species
  • the structure and function (including typical species) of qualifying natural habitats
  • the structure and function of the habitats of the qualifying species
  • the supporting processes on which qualifying natural habitats and the habitats of qualifying species rely
  • the populations of each of the qualifying species
  • the distribution of qualifying species within the site

Qualifying features

Refer to the site information table above for the list of features within this site.

This should be read in conjunction with the accompanying supplementary advice section, which provides more detailed information to help achieve the objectives set out above, including which attributes should be maintained and which restored.

The conservation objectives apply under the Habitats Regulations, and must be considered during a Habitats Regulation Assessment, including an Appropriate Assessment.

The conservation objectives and accompanying supplementary advice provide a framework to inform the management and measures needed to conserve or restore the European site, and the prevention of deterioration and significant disturbance of its qualifying features.

Where the objectives are met, the site will be considered to show a high level of integrity, and to be contributing to achieving the aims of the Habitats Regulations.

Supplementary Advice on Conservation Objectives

See supplementary advice on conservation objectives for this site, which aim to describe the range of ecological attributes that are most likely to contribute to a site’s overall integrity.

Last updated: 13th September 2019

Advice on Operations

See the advice on operations for this site to view information on the sensitivity of features in this site to the pressures exerted by different activities.

Last updated: 13th September 2019

Advice on Seasonality

See the advice on seasonality for this site, to view the months in which each mobile feature occurs in this site.

Last updated: 15th March 2019

Feature Condition

In 2016, Natural England trialled and rolled out a new Marine Protected Area (MPA) condition assessment methodology that provides robust results and information on the condition of marine features designated within MPAs in England. With guidance from National teams and using all available evidence and condition monitoring data, Area Teams conduct these assessments following a standardised approach that assesses if the feature and sub feature conservation targets set for each MPA have been met.

To date, condition assessments have been completed for a number of features in a range of marine Special Areas of Conservation (SACs) by the National and Area Teams. Further marine habitat features in SACs and other MPAs will continue to be assessed in the future. The new method can now also be applied to complete habitat and species condition assessments for other MPAs in England, whilst still meeting the different processes in place to report on the results of condition of features in Marine Conservation Zones (MCZs) and Special Protection Areas (SPAs). Different processes are currently in place to decide and report on the condition of non-marine habitat and species features of SACs.

The main part of the assessment process is directly undertaken and stored here on Natural England’s Designated Sites View. The details for the most recent assessments of this site can be found here.

Management measures

If you are carrying out an environmental assessment, planning an operation or assessing an operation or proposal, it is important to consult with the following organisations where applicable. To find out if any management measures, byelaws or other restrictions apply to your activity see the management measure page or you can use the following links for more information.

The Marine Management Organisation license, regulate and plan marine activities in the seas around England and Wales so that they’re carried out in a sustainable way.
Environment Agency are responsible for regulating major industry and waste, water quality and resources, fisheries, inland river, estuary and harbour navigations, conservation and ecology.
Offshore Petroleum Regulator for the Environment and Decommissioning (OPRED) regulates oil and gas, CCS and gas storage activities in the marine environment.

Further information

For further information relating to this designated site you can refer to the following resources:
Site specific information: Other information:
For further information about this site contact: Natural England enquiries Telephone: 0300 060 3900. Email: