The Ay and Rhun Islands Marine Protected Area (MPA) in Maluku, Indonesia, demonstrates how climate adaptation and traditional management can be integrated into marine conservation. Part of the globally significant Banda Islands, the area supports diverse coral reefs, seagrass, sea turtles, napoleon wrasse, tuna, and marine mammals, including blue whales. The Coral Triangle Center (CTC), together with the Ministry of Marine Affairs and Fisheries, the Maluku Provincial Government, customary leaders, and local communities, conducted ecological and socio-economic assessments, stakeholder consultations, and participatory zoning that led to the MPA’s establishment in 2021. The design incorporates climate resilience principles, including protection of resilient reefs, habitat connectivity, replication, and upwelling systems, while revitalizing the traditional Sasi system. This science-based and community-led approach strengthens biodiversity conservation, food security, climate resilience, and effective ecosystem management.