<p>Coral reef fisheries and small pelagic fisheries make different contributions to livelihoods, food and nutrition security, which have informed academic and policy debate about their respective needs for governance. However, few studies have explicitly examined how governance of these different fisheries interacts at a local level, or how they interact with wider social-economic contexts and processes. This study examines a small pelagic fishery in the Philippines, focusing on the varied interactions between this fishery and coral reefs. Drawing on household surveys, focus group discussions and interviews, we demonstrate the significant economic and social contributions made by the small pelagic fishery and describe a series of governance interventions aimed at protecting coral reefs and regulating small pelagics. We highlight some of the emerging governance risks that undermine legitimacy and social acceptance for the management of both small pelagic and coral reef resources. We argue that planning for successful management of fisheries needs to be highly cognizant of the complexity of livelihoods, to equity issues in sharing the benefits and burdens of conservation, and to tourism-fishery interactions.</p>