Mayalibit Bay Marine Protected Area (MPA) has an area of 53,100 hectares and almost splits the island of Waigeo into two parts. Mayalibit Bay has vast mangrove and seagrass habitats, with seagrass spreading across 70m from the edge of the mangrove forest to the coast. Although the percentage of hard corals is relatively small, Mayalibit Bay has great potential as an area for economically significant fish to grow to large sizes. These species include mackerel (Scombridae), samandar (Siganidae), shrimp, bubara (Carangidae), snapper (Lutjanidae) and mud crab (Scylla). The main commodities are mackerel (Rastrelliger sp.) and dried shrimp, in fact, Mayalibit Bay is famous for its mackerel. Almost all mackerel fish consumed in Raja Ampat comes from Mayalibit Bay. Study results have shown that the mouth of the bay is an important spawning ground for the species.
Mayalibit Bay belongs to the ancient Mayan tribe, indigenous to Raja Ampat. Administratively, the bay is divided into two districts namely Mayalibit Bay and Tiplol Mayalibit, with a total of 10 villages between the two districts. Data from 2012, states that there are 1,796 people living throughout the bay. Out of the 10 villages, three villages are Muslim and the rest are Christian. Similar to other areas in Raja Ampat, Mayalibit Bay has also suffered from decreasing fish resources due to unsustainable and overexploitive fishing.
On November 15, 2006, the Mayalibit Bay community performed a custom declaration in the village Waifoi, handing over the local mandate to manage the region's fish stocks to ensure sustainability, to the Raja Ampat government. The custom declaration was then followed by a declaration at the district level by the Regent of Raja Ampat, Drs. Marcus Wanma (M.Si), endorsing the MPA with an area of 53,100 ha, along with five other MPAs, namely South-East Misool, Kofiau, Strait Dampier, Wayag and Ayau Asia. The declaration at the district level was also marked by the publication of the regent decree (Perbub) No. 66 of 2007 and later the regional reguegulation (Perda) No. 27 of 2008.