Global warming, overfishing, and coastal pollution are main drivers of marine ecological changes in developing countries, such as Indonesia. Marine Spatial Planning (MSP) prioritizing the establishment of Marine Protected Areas (MPAs) is the local mitigation to reduce the effects of marine ecological changes. It has been acknowledged that MPAs play important roles in: (1) reducing the effects of global warming via uptaking and storing carbon into sediments, (2) protecting marine lifes via providing suitable habitats and maintining natural behaviors, (3) supporting coastal fisheries via exporting adult fishes and larvae, and (4) reducing the effects of coastal pollution via enhancing water and sediment quality. In order to gain maximum benefits, MPAs should meet four standard criteria: (1) representation, i.e. MPAs should cover all marine ecosystems (e.g. mangroves, seagrass beds, and coral reefs), (2) replication, i.e. MPAs should be established in many sites, (3) geographycally widespread network, i.e. among MPAs should be connected, and (4) self sustaining total area, i.e. MPAs should be large enough to support ecological processes.