In this review, the biodiversity of the coastal marine regions of the Indian Ocean is contrasted with that of the Pacific and Atlantic oceans. We discuss the important types of coastal habitats (coral reefs, mangrove forests and seagrass meadows) in the Indian Ocean and their use as proxies for biodiversity. An overview of what is known of coastal marine biodiversity in different parts of the Indian Ocean is assessed by using comparable information on some of the better-known taxonomic groups, including corals, mangroves, seagrasses, fishes, marine mammals, turtles, crustaceans and molluscs. We also discuss important gaps in our knowledge and aspects of the biodiversity that will never be determined either because of changes that have already occurred or because we cannot increase our knowledge at a rate relative to anthropogenically induced change. A framework is proposed for the Indian Ocean based around international cooperation to increase our understanding of biodiversity based on ecosystem bioregionalisation and linkage of this to mechanisms ensuring protection of important and representative areas of coastal marine biodiversity.