Distribution patterns of corals of the genus Acropora in Indonesia are examined for the contribution they can make to the management and conservation of Indonesia's coral reefs. The Indonesian Archipelago contains the greatest recorded diversity for the genus worldwide (91 species). Distribution patterns indicate that regional differences occur within the archipelago and that these are influenced by an overlap of Indian Ocean species distributions diminishing eastwards and a stronger pattern of Pacific Ocean species distributions diminishing westwards under the influence of the Pacific through-flow current. Eighteen percent of Acropora species within the archipelago are restricted to designated regions. This strong biogeographical demarcation is complemented by a diversity of Acropora within the archipelago due to the occurrence of a broad range of reef types and contrasting environmental conditions. Results of this research suggest some Acropora fauna is restricted to particular reef and habitat types in designated regions. This new information has important implications for the origins of coral distribution patterns, the interconnectedness of coral reef environments, and the importance of habitat diversity to conservation. Such information can be used to inform management, and when combined with data from other marine organisms, can provide strategic guidelines for the conservation of coral reefs in Indonesia.