The Western Indian Ocean results from a complex geological history, implying both plate motion since about 180 million years and volcanic hot-spot activity since about 68 million years. This region exhibits a myriad of islands different in nature and origin, including continental remnants (Madagascar, the granitic Seychelles), high volcanic islands (Reunion, Mauritius, Rodrigues, the Comoros), high- and low-lying carbonate reef platforms (the carbonate Seychelles, the French Scattered Island Group, Agalega Islands) and a few submerged reef banks (Geyser, Nazareth, Saya de Malha). This region contains all known types of reefs—fringing, barrier, atoll, platform and bank. The data about reef development history over the Quaternary were gained mainly from two distinct sources: boreholes and emerged outcrops. Reef drilling indicates that modern reefs started regionally to grow from about 10,000–9600 years BP. Rates of vertical reef accretion ranges from 0.2 to about 10 mm/year according to exposure and shape of coral builders. The sea-level curves, reconstructed from vertical reef-accretion and lagoon-deposition curves, express a rapid rise in sea level at rates averaging 6 mm/year between 10,000 and 7500–7000 years BP, with a stabilization at the present position around 2500–3000 years BP. There are significant variations in the composition and distribution of dominant reef-building coral assemblages and facies (framework versus detritus) according to exposure to wave energy. Frameworks composed of robust coral branching assemblages—mainly Acropora robusta, A. humilis groups; Isopora palifera—dominate in higher energy settings, while those with domal and tabular branching forms—mainly Porites, various faviids, Acropora hyacinthus group—are best represented in lower-energy to protected environments. Detritus-reefs are best developed in sheltered sites. The recent contribution of some dominant coral species in modern WIO reefs seem to have resulted from their delayed arrival in the region as controlled by the regional prevailing surface circulation—South Equatorial Current and Agulhas Current—and/or by the competency period of their larvae. Coral-based, geochemical records suggest that, during the mid Holocene, the seasonal variability of sea surface temperatures was lower than today. The reconstruction of the WIO Pleistocene reef history is chiefly based on a limited number of exposed reef remains deposited during the last interglacial MIS 5.5 stage (129,000–125,000 years BP), at present culminating at elevations ranging from − 20 to + 9 m with respect to present mean sea level. Such differences in elevation can be explained by a differential tectonic behaviour of reef-bearing substrates, from stable continental areas to subsiding volcanic islands. The existence of older reef generations (Plio-Pleistocene) was identified from coral-rich inclusions trapped into pyroclastites of Comoro volcanoes.