Regional decentralization has made a change to any development sectors where a region (regency/town) holds a broader authority in managing natural resources, including watershed. Watershed management will run well if there is coordination and policy integration between the central and local government and between related institutions within a region. Relationship between institutions shall be always built on a coordination in order to prevent overlapping and conflict of interest in watershed management. The study aims to collect the data/information on main duties and functions of, authority of and roles of watershed management institution, especially the watershed in Ambon City, Leitimor Peninsula and to analyze them through stakeholder analysis approach. The findings found seventeen stakeholders who are in charge of the watershed management. Among those stakeholders, the primary and most important watershed managers are the Watershed Forum and forest farmer group.