The Inner Islands are the centre of activity and are based on a shallow granitic plateau, a relic from the pre-historic super continent of Gondwanaland; the majority of the islands are mountainous with a few outlying coral islands at the edge of the plateau. The main island of Mahe with the capital city of Victoria is home to most of the resident population followed by Praslin, and La Digue. The majority of the tourism facilities are based on these islands and consequently most of the diving in the area has been from the land based dive centres on these islands, although some Liveaboards now offer programmes in this area. Being on a granite plateau the sea depths tend to be 40 metres or less and underwater scenery is characterised by granite reefs encrusted with coral formations as well as true fringing reef structures. This area is North of the cyclone belt with a climate moderated by the trade winds and dominant mountains that promote year-round diving conditions.

The Amirantes are a group of coral islands and sand-bars to the South West of the Inner island group; strictly speaking they comprise the Amirantes group to the north and the Alphonse group to the south. These islands are true "coral islands" and are the coral crowns of submerged mountains; the underwater terrain is very different to the inner islands with coral walls and steep drop-offs to several thousand metres in depth. This area is on the outer fringe of the cyclone belt and is accessible at only limited times of the year, September to May and tends to have a much drier climate that the Inner Islands. There has been very limited tourist infrastructure developed in this area with Lodges on Desroches and Alphonse only. 

To the South and South West of the Amirantes, now some 10 degrees South of the Equator, are the Southern Islands, which comprise the Farquar and the Aldabra groups of islands. These islands are on the edge of the cyclone belt and have been subject to infrequent cyclone passage which occur mainly in January. Accessibility is thus limited to Mid October to Mid December and then again in March to the end of April. These coral atoll formations include the UNESCO World Heritage Site of Aldabra, the largest raised coral atoll in the world and home to over 120,000 giant land tortoises amongst other rare and endemic animals.