This paper presents the challenges and opportunities of small-scale fisheries management in Misamis Occidental, especially in the coastal municipalities of Aloran, Jimenez, Lopez Jaena, Panaon, Plaridel, Sinacaban, Tudela, and Oroquieta City. A site diagnosis was conducted as part of the participatory diagnosis and adaptive management framework to characterize the governance of small-scale fisheries in the area and to determine the potential for adopting the ecosystem approach to fisheries. Stakeholders identified, in order of priority, the following issues affecting fisheries and coastal resource management in Iligan Bay: depleted fishery resources, lack of alternative livelihood, and limited institutional capabilities. In a united response, the local government units in the area formed the Iligan Bay Alliance of Misamis Occidental, through which they explore opportunities to address issues and to restore and sustain the fisheries in Iligan Bay.