The low coralline islands to the south and west of the Seychelles Bank fall into a number of geographic groups. The largest is that of the Amirante islands, which extend along a shallow north-south ridge, with the Alphonse group forming a slightly separate southern section of this chain. Further south are two small and more disparate island groups, Those of Providence-Farquhar and the Aldabra Group. Finally, directly to the south of the Seychelles Bank are the isolated islands of Platte and Coetivy. The reefs in these outer island areas are highly varied, and include true atolls (St. Joseph, Alphonse, Farquhar), raised atolls (Aldabra), submerged or partially submerged atolls (Desroches, Coetivy), and platform or bank structures (African Banks, Providence-Cerf). Coral cover varies considerably between localities, ranging from close to zero on some banks and reef slopes (notably the large Providence-Cerf Bank), to 60-70 percent on some atoll slopes.

The Seychelles islands have an estimated 1690 km2 of coral reef, which is about 13.1% of the total coral reef area of the Eastern Africa and the South West Indian Ocean islands. The inner islands, where most people live, have only 40 km2 of coral reef, and fishing remains the most important economic reef activity. Reefs around the granitic islands are heavily fished and yield around 50% of the total annual demersal catch. In 2003, it was estimated that 19% of visitors to the Seychelles participated in scuba diving and 65% in some form of snorkelling activity. Prior to the mass coral bleaching event of 1998, the coral reefs of the Seychelles were described as healthy with high coral cover, typically 60-90%. Coral cover after the bleaching event was reduced to less than 5% at most locations around the granitic islands. Between 2000 and 2004 mean live coral cover increased from 3.7% to 10.2% and is still increasing. Primary threats to coral reefs include dredging and reclamation, sedimentation, excessive fishing pressure, coral diseases, invasive species and climate change associated with global warming.