The Reformation Era, Indonesia decentralized a number of new authorities. However, after fifteen years of regional autonomy, the authority to manage natural resources at the sea was transferred from the regency/city government to the provincial government. Re-centralization of this authority has an impact on cross-provincial Intergovernmental Cooperation Institutions (IGC), marine and fisheries sector, which has been carried out for five years. This case study highlights the policy of transferring authority from the regency/city to the provincial government, and the impact on crossprovincial local IGC Institutions "PAWONSARI", is the cooperation of three regency from three provinces: Pacitan-Regency, East Java, Wonogiri-Regency, Central Java and Gunungkidul-Regency, Yogyakarta Special Region. Findings point to the local IGC institutions has succeeded, instead has not functioned optimally, because of the policy recentralization of local authority. We argue the importance of a new approaches in cooperation to ensure the involvement of local stakeholders and political stability.