Abstract: M Marine Protected Areas Management based regional authority indigenous peoples and Local Government Raja Ampat, is now faced with a potential structural conflict based on the authority of the Ministry of Maritime Affairs and Fisheries (MMAF) with the issuance of the Decree of the Ministry of Marine and Fisheries No. 65 of 2009. One year after enactment Raja Ampat Regency No. 27 of 2008. the issuance of Decree No. 65 year 2009 CTF, has given birth and are the source of their vertical conflicts related to the regulatory authority of the Ministry of Maritime Affairs and Fisheries with the Raja Ampat Regency Government as the recipient of the mandate of indigenous peoples Raja Ampat in the context of the Regional Marine Conservation Area Management in Raja Ampat.