Aerial view of the reefs around Mayotte in the Comoro archipelago. Fringing reefs grow around the island shoreline. The offshore barrier reef started growing when sea level was lower, as a fringing reef around a much larger island.
© David Obura

A typical shallow coral community dominated by fast growing Acropora (staghorn) corals.
© Cheryl-Samantha Owen/

Corals grow up to sea level building up the reef framework over several hundreds to thousands of years, forming all the reef types - fringing, barrier, atoll and banks.
© Cheryl-Samantha Owen/

A revised view of coral diversity in the WIO, where diversity in the northern Mozambique channel (NMC) is higher than sites to the north, south and east in the islands.
© David Obura

Coral reefs

Coral reefs in the WIO extend from the most northern parts of the Indian Ocean to the South African coast at 32°S. They are found along the continental coastlines of East Africa and Madagascar where there are no major river systems, on all the small islands, and on parts of the submerged banks that are both shallow enough and have some variation in topography. They are intimately associated with seagrass beds, with much of what is called ‘coral reef habitat’ being flat open seagrass and sand beds in between rocky outcrops and true reef structures. In sheltered locations mangrove stands are often associated with reef and seagrass habitats, though the high-sediment and freshwater conditions supporting the largest mangrove systems in East Africa prevent the growth of immediately adjacent coral reefs. The coral reef fauna of the WIO is a mainstream component of the Indo-Pacific region, with very high faunal affinities stretching across the Indian Ocean to the southeast Asian and West Pacific regions. However, new insights into the fossil record of reefs is raising the possibility of a distinct evolutionary history of coral reefs in the WIO, and by extension, of other shallow marine habitats and their species, raising the possibility of a unique regional fauna.

Reef geomorphology - Charles Darwin first described the process of transition from fringing to barrier to atoll reefs, partly from observations in the Indian Ocean, including the Chagos archipelago and Aldabra atoll. The WIO has a variety of offshore bank reefs and island/continental reef systems, representing a full range of reef formations :

  • fringing reefs are found around all the islands and the East African coast;
  • barrier reefs are most strongly developed at Tulear (Madagascar) and around Mayotte (which also contains a second/inner barrier within its lagoon), and partially developed or poorly known in several locations - the west coast of Mauritius (Mahebourg), south side of Mohéli (Comoros);
  • atolls are found in the Seychelles (e.g. Aldabra, Cosmoledo, Farquhar, Alphonse) and in the Iles Éparses (Europa, Bassas da India), and submerged atolls at Zélée and Geyser;
  • coral banks are numerous, such as those offshore of major coastlines (e.g. Malindi – Kenya, Leven and Castor – NW Madagascar, African Bank – Mozambique), and the very large banks of the Mascarene Plateau - Cargados Cajaros, Nazareth and Saya de Malha, and the North Seychelles Bank.

The Millennium Coral Reef Mapping Project developed a single global classification of geomorphological classes for reefs, defining 800 different classes. Application of this method to the WIO islands conducted by the RAMP-COI project resulted in identification of 199 classes (25% of the global geomorphological diversity). Madagascar had the highest diversity with 86 geomorphological classes, followed by Seychelles and Mauritius with 54 and 53 classes respectively, then Mayotte (42), Comoros (28), the Iles Éparses (16) and Reunion (4). Using these classes, the sum of reef and non-reef areas in the islands equaled approximately 14,000 km² and 50,000 km² respectively. Madagascar and Seychelles had the largest reef areas, with 5000 and 5400 km² of reef area respectively. The atolls, banks and islands had approximately 9000 km² of reef. The Seychelles Bank alone represents 42,800 km² of non reef area. The East African continental coast has not yet been classified.

Corals - Continental reefs in the WIO are distinguished from other Indo-Pacific reefs by the dominance of mono-specific stands in genera such as Galaxea, Lobophyllia, Montipora and Porites. More typical Indo-Pacific reef assemblages are also common on the islands and mainland, dominated by branching corals in the genera Acropora and Isopora, and mixed communities including genera in the families Faviidae, Mussidae, Petiniidae, Fungiidae and others. Endemic coral species in the WIO (with the ranges of some extending to the northern Indian Ocean) include Ctenella chagius, Craterastrea laevis, Horastrea indica, Gyrosmilia interrupta, Anomastrea irregularis and Parasimplastrea sheppardi with the first two species only recorded recently from Chagos and Mauritius, and Mayotte and Madagascar, respectively.Regional endemics that are so rare they have not been recorded in decades include Astreosmilia, Erythrastrea and Machadoporites. The taxonomic position of these species is in question, raising the possibility of endemism at higher taxonomic levels than previously thought, and a unique lineage of corals in the Western Indian Ocean. Recent genetic research has shown that the genera Stylophora and Siderastrea have ancestral species in the WIO/Red Sea region compared to younger species farther east in the Pacific, and in the former case, higher levels of genetic diversity in the WIO/Red Sea. These results are also suggestive of so-far-unknown levels of diversity in the WIO and a distinct evolutionary heritage compared to the broader Indo-Pacific.

Significance - Coral reefs are among the most biodiverse of marine ecosystems, with 93,000 species of coral reef organisms currently described, of which some 4,000 are fish and 800 are corals. Depending on assumptions, scientists estimate from 1-3 million species may depend on coral reefs, representing as much as 25% of marine biodiversity.


  1. Reefs at Risk country estimates reported in Spalding et al. 2001. Country estimates were not given in Reefs at Risk revisited, in 2011.
  2. reef areas are obtained from the World Atlas of Coral reefs, and for the islands (to the right of the ‘/’) from the Millenium Reef Mapping project. Differences in these numbers reflect different methodologies and assumptions about reef habitats and structure.
  3. the first numbers are two sources: mainland sites- Spalding et al. 2001 (World Atlas of Coral Reefs) based on Veron (2000) estimates, based on predicted numbers of species; island sites- Pichon 2009 based on  based on field surveys and literature) for RAMP-COI. The second number is predicted species richness based on field surveys (Obura 2012) and are likely underestimates of true diversity. Discrepancies between these numbers are based on differences in methods and sources of information.
  4. numbers of marine protected areas with coral reefs in Madagascar and Mozambique have increased greatly since the source report publication date, these numbers incorporate estimated increases. Mayotte: only one MPA covering the entire EEZ (with 6 more strict MPAs)

Coral reefs support a high diversity of other taxonomic groups, such as those dependent on the corals themselves for habitat. For example damselfish (top) and crustaceans (below) have adapted to live among coral branches.
© Melita Samoilys (top) / © Keith Ellenbogen (below)

Combined threats to reefs in the WIO, ranging from red (high) to blue (low)
© Burke et al. 2011

Susceptibility to thermal stress, with darker colours indicating higher suscptibility and risk of coral bleaching
© Maina et al. 2008

Status of WIO coral reefs in 2008 (GCRMN)

More than 500 million people worldwide depend on coral reefs, and this number may be approximately 15-20 million in the WIO. Direct uses of reef resources include extraction of fish, invertebrates and algae for food and other goods such as for building and pharmaceuticals, recreation and the tourism industry, and as physical infrastructure for maritime transport and coastal protection. For coastal communities and societies, reefs may have cultural and spiritual significance. Reef resources and services are worth an estimated 375 billion dollars each year globally, with estimates ranging from U$ 2,000 to >100,000 per ha/year for reefs in the WIO, depending on whether they support artisanal fisheries (at the lower end) to urban coastlines and tourism industries (at the higher end).

Threats - Coral reefs are highly valued for their ecosystem services, so experience significant use and threat levels throughout the WIO. The exploitation of marine resources, urban pollution, terrigenous sedimentation, coastal development and tourism are among the main anthropogenic pressures that cause degradation of ecosystems in the region. A classic example of the combined effects of these stresses is the Grand Recif at Tulear – the largest barrier reef in the Indian Ocean, which in the last 40 years has been degraded to a state of virtual death of the reef system, and the loss not only of ecosystem function, but of many species, including reef-building corals. Artisanal and small scale commercial fishing, and urban pollution and massive sedimentation are all implicated in this loss.
Fishing pressure is increasing in all countries with increasing local and global populations, and globalization of fisheries is resulting in mounting pressures to even the remote mid-ocean reefs and banks. Destructive fishing such as with small-mesh seine nets, poison and dynamite are pervasive where national governance mechanisms fail to keep them under control. Threats from pollution are less severe in the WIO than elsewhere, reflecting the low levels of industrialization and maritime trade by global standards, though these are increasing.
The growing global energy demands has led to increased exploration for oil and gas within the WIO (Kenya, Tanzania, Mozambique, Madagascar and Seychelles). Exploration leases off the coast and onshore sedimentary basins cover the entire west coast of Madagascar and parts of the east coast. Currently, exploration results indicate significant reserves of heavy oil and the possibilities of lighter crude and gas. Extraction of these reserves will pose a serious threat to reefs and other ecosystems.
Climate change is now recognized as one of the greatest threats to coral reefs worldwide, particularly from rising sea surface temperatures, and ocean acidification. Coral bleaching has led to substantial damage to coral reefs on a global scale (16% of reefs suffered lasting damage in 1998 alone), with some parts of the western Indian Ocean losing 50-90% of their coral cover (e.g. Kenya, Tanzania, Seychelles, Mayotte).
Regional studies of coral bleaching have revealed differential histories of bleaching, indicating high- and low- vulnerability regions to potential future climate change. Reefs in hot stable temperature regime waters in the east of the Mozambique channel and the Seychelles, and in cooler but more variable regions in Kenya have suffered greater bleaching in the past. Regions with slight cooling from upwelling and oceanographic influences – along the Mozambique coast, or in the Mascarene Islands have suffered less bleaching, or more variable levels of bleaching. For the Indian Ocean as a whole, 65% of reefs are at risk from local and global threats, rising to >85 % by 2030.

Management, mitigation and restoration - The two existing World Heritage marine sites in the WIO, Aldabara and iSimangaliso, both contain coral reefs making them among the best-represented habitats so far on the World Heritage list in the WIO. This is also true globally, where almost half of the 45 marine World Heritage sites contain coral reefs as a significant feature.
Coral reefs are strongly impacted by local threats, thus targeted management at local scales is the most successful course of action for conservation. Fisheries management, to reduce the proportion of fish stocks extracted, area-based management in MPAs, to protect key locations, breeding stocks and a proportion of total habitat area, and Integrated Coastal Zone Management, to reduce land-based impacts on coral reefs are the three main tools.
MPAs have been extensively applied in the WIO with a focus on coral reefs. In the islands, there are currently over 51 marine protected areas (parks and reserves) and fisheries reserves representing around 5000 km², plus two whole-EEZ MPAs designated in 2011 and 2012, in Mayotte (70,000 km²) and Glorieuses (48,000 km²).  On the mainland, a consistent audit of MPAs has not been done recently, though Kenya, Tanzania and South Africa have up to 10% of their territorial waters under some form of area-based protection. Most management areas, and certainly the large ones, are under government control, with increasing popularity of community –managed areas in the last decade, though these are mostly small in size.
With the advent of climate change as the most significant region-wide threat to coral reefs, and limited ability of regional countries to contribute to global efforts to reduce greenhouse gas emissions, commitment to local actions to buy time for corals to adapt and acclimate to the changing climate is essential. Thus management actions and planning to maximize protection to reef areas and corals that have high resistance to warming, and to preserve the features that promote recovery following mass mortality of corals are essential. Regional planning and coordination are necessary to support these, as coral reefs are connected at regional levels.
Restoration for degraded reef communities is not yet at a level where action can be taken at meaningful ecological scales. Restoring the conditions that promote natural recovery – adequate herbivore and consumer populations, a clean environment and connectivity corridors – as can be done with well-planned MPAs, fisheries and coastal management is more important at scale than attempts to manipulate local reefs such as through replanting of corals.

Key References - Allen (2008); Andréfouët et al. (2009); Ateweberhan & McClanahan (2010); Carpenter et al. (2011); Chen et al. (in prep); Conservation International (2008); Flot et al. (2011); Griffiths (2005); Hamilton & Brakel H (1984); Maina et al. (2008); McClanahan et al. (2007)b); Obura (in review); Obura et al. (2007); Pichon (2008); Rosen (1971); Sheppard (1987); Spalding et al. (2001); Stefani et al. (2011); Veron (2000); Wafar et al. (2011); Wilkinson (2000)/(2004)/(2008). --> References