In terms of history, Raja Ampat Archipelago in the 15th century was part of the reign of Tidore Sultanate, a great kingdom centered in Maluku Islands. To run its government, the Sultanate of Tidore appointed 4 local kings to rule in the the island of Waigeo, Batanta, Salawati and Misool which were the fourth largest island to this day. The term 4 Kings who rule the islands becomes the root of the name Raja Ampat.

The regency which celebrated its anniversary on 9th May is now a Regency in the province of West Papua expanded from Sorong regency in 2003. As we look at the map of West Papua Province, this regency is situated in the western island of bird-beak like papua island. Raja Ampat consists of approximately 610 islands with a total length of 753 km coastal lines. The center of government and also the capital of Raja Ampat Regency is a city situated in Waigeo island, the city Waisai.