Marine Protected Areas (MPAs) are widely considered to be one of the best strategies available for protecting biodiversity and ecosystem processes in marine environments,
particularly in developing, tropical nations. While data on connectivity and genetic structure of marine populations are critical to designing appropriately sized and spaced networks of MPAs, such data are rarely available. Here we present an assessment of genetic structure in reef- building corals from Papua and West Papua, Indonesia, among the most biologically diverse and least disturbed coral reef regions in the world, and the focus of the multi-institutional Bird's Head Seascape initiative to design and implement a functional network of MPAs.