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Merauke Regency is a plain area which is between 0-60 meters above sea level and the south and west are bordered by the Arafuru Sea. Flat areas become centers of population that use land for cultivation activities and become a concentration of settlements. While the coastline of the Merauke Regency is potentially developed into a maritime-based tourist destination, which is often called Marine Ecotourism. The research objectives are: designing a strategy for developing marine ecotourism in Merauke Regency. The research method used is the purposive sampling research design, expert system research methods, and analysis techniques with the Analystical Hierarchy Process (AHP). The conclusions in this study are: (a) Priority goals is: the preservation of sustainable coastal resources especially mangroves, growing a new center of economic growth, preparing the location of new marine tourism destinations, increasing the contribution to local revenue, ( b) The priority of the main actors is: private, private together with the government, and government, (c) The development faculties are: structuring of coastal areas and exploitation of sand and mangroves, structuring of acceptance to marine tourism areas, integrated socio-economic engineering and technology, developing fishery-based agro-industry SMEs, and promoting and attracting investors for the development of marine tourism.