The reefs of the Mascarenes differ in structure and stage of development. Mauritius is the oldest island, bound by a discontinuous fringing reef and small barrier reef, with large lagoon patch reefs. Rodrigues has nearly continuous fringing reefs bounding an extensive lagoon with deep channels and few patch reefs. Reunion, the youngest island, has short stretches of narrow fringing reefs along southwestern coasts. The islets of St Brandon are bound to the east by an extensive arc of fringing reef. Reef mapping of the Mascarenes using satellite imagery provides an estimate of 705 km2 of shallow reef habitats. These areas have been modified over geological time by changes in sea level, ocean-atmosphere disturbances and biological and chemical forcing. Further modification has resulted from historical changes in land-use patterns. Recent economic development has placed many of these reefs at risk from anthropogenic impact. The reefs of the Mascarenes have escaped mass mortality from bleaching to date, which increases their conservation significance within the wider Indian Ocean. The reefs are poorly protected. A case study shows how a geographic information system incorporating reef-habitat maps can help formulate and demonstrate Marine Protected Area boundaries.