This paper summarizes an integrated method for selecting Marine Protected Area (MPA) sites and presents empirical evidence that illustrates how an MPA that was largely conceived using indigenous ecological knowledge and existing sea tenure governance (i.e., customary management practices), as part of a regional precautionary and adaptive community-based management plan, is showing signs of biological and social success. The paper shows how hybrid natural and social research approaches in tandem with customary management for designing MPAs can protect coral reefs in Oceania.