Raja Ampat is a national and global priority for conservation as it contains the world’s most diverse coral reefs and critical habitats for globally threatened marine species, and is a cetacean migratory corridor. As a result local governments in this region are facing difficult decisions in their attempt to balance sustainable development with conservation of globally significant marine diversity. This report describes a process conducted to support the development of zoning plans for Raja Ampat’s MPA network. Activities undertaken included developing a spatial database on species, habitats and human uses; engaging stakeholders through a series of meeting and workshop; applying state of the art conservation planning tools to synthesize information and examine trade-offs.