This paper discusses the impact of local and national policies in the Philippines on the participation of indigenous peoples in relation to fisheries management. Specifically, this research focuses on the Tagbanua, an indigenous group in Coron Island, Palawan, on the western side of the Philippines. The struggle of the Tagbanua in reclaiming their ancestral title to the land and sea reflects broader moves toward self-determination, which is critical not only to their ancestral lands and waters, but also to their survival. Indigenous rights are essential in addressing social justice and in giving a greater voice that encourages indigenous peoples towards self-governing institutions and common management of resources. While the basic premise assumes that the right to access and control of ancestral domain is critical to the indigenous peoples (IPs) in the Philippines, this paper addresses the following questions:(1)What does property rights mean to indigenous peoples who have been historically dependent on their natural resources?; (2)What level of organization or institutional mechanism is viable in the management of fisheries for IPs?; and (3)In the context of fisheries management, how should we integrate property rights with indigenous rights? Significantly, the fundamental development of indigenous peoples lies in the recognition of their rights in their ancestral domain and the preservation of their culture, tradition, system, practices and their natural resources. This paper examines the Tagbanua experience, through a critical exploration of institutions and property rights, with attention to corresponding effects in reducing conflict with other stakeholders in the area, and in affecting the sustainability of fishery resources.