Understanding how institutions operate is crucial to the protection of marine ecosystems and the communities that depend on them. We define institutions as the rules, norms, and practices that govern resource users’ interactions with common-pool resources, and recognize that both formal and informal institutions govern marine fisheries around the world. Institutional diversity can enhance social-ecological system resilience by providing multiple ways of responding to change. Identifying institutions and their effects on fishing practices is key to improving management for sustainable fisheries. In this study, we use a mixed methods approach focused on the institutions guiding fishing activities of the Mexican chocolate clam, Megapitaria squalida, in Loreto Bay National Park, Baja California Sur, Mexico. By synthesizing long-term observations and semi-structured interviews with fishers and other key stakeholders, we identify the formal and informal rules and norms governing fishing behavior, explore their effects on fishing practices, and illuminate ways in which formal and informal institutions may work in tandem. We find that both formal and informal institutions shape fishing practices within the chocolate clam fishery. Some reinforce one another, and others are in conflict. The diverse institutions governing the chocolate clam fishery create a complex web of sometimes conflicting rules and social norms that fishers navigate every day. We contend that greater community participation in management, via polycentric and collaborative governance that accounts for and legitimizes local norms in a system like co-management, would foster enhanced sustainability of the chocolate clam fishery and the benefits it provides to coastal communities.