“Geographic priorities for marine biodiversity conservation in Indonesia” represents the first comprehensive review of Indonesia’s marine conservation priorities since 1984’s landmark “Indonesia Marine Conservation Data Atlas,” produced for the Indonesian Department of Nature Conservation by IUCN and WWF. With Indonesia’s international commitment to both the Coral Triangle Initiative and achieving a goal of 20 million hectares of marine protected areas by 2020, we were tasked to provide a scientifically comprehensive geographic prioritization strategy to guide these efforts. The prioritization exercise reported in this document was designed to fulfill this request.