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Abstract: The distribution of species in their environment is largely defined by habitat characteristics. Both species and habitat distributions can be used to define conservation areas, especially in highly diversified ecosystems like coral reefs where biodiversity inventories are lacking. The main objective of this study was to test the relationship between multi-taxa community structure (defined by richness, species lists, and taxonomic distinctness) and habitat typology in the Man and Biosphere UNESCO Reserve of Baa Atoll (Maldives). Species richness per taxon was described at 18 stations located on different habitats mapped using high resolution satellite imagery. A total of 1012 species were described including 178 macroalgae, 173 corals, 121 hydroids, 351 fish and 189 (other) macro-invertebrates. Rarity was extremely high for macro-invertebrates, algae and hydrozoans. The results highlighted a marked difference in species composition between stations for macro-algae and corals but not for other groups (hydroids, fish and macro-invertebrates). These distribution patterns were not strongly correlated to differences in habitat characteristics, which created a weak spatial structure of communities between habitats probably caused by differential exposure of atolls to monsoons and the 1998 bleaching event. Community differences between stations were often due to rarity. Therefore, identifying a network of protected areas that includes occurrences of all species may pose challenges. This is overcome by conservation planning scenarios using medium-size (of the order of 1km2) management units. [Copyright &y& Elsevier]