This paper reports on the outcomes of a project that engaged researchers and fishers together in adapting participatory social science approaches to the purposes and the constraints of community-based fisher organizations. The work was carried out in the Scotia-Fundy Region of Atlantic Canada (the Bay of Fundy and Scotian Shelf) between 1999 and 2003. After a period of reflection on what was collectively learned from our experiences in this project, the academics went back to the community partners in a recent workshop for further discussion and refinement of the lessons. We conclude that true participatory fishery research, utilized in support of community-based management, can be a particularly powerful tool. However, it has few effective shortcuts, it must deal early in the research process with power imbalances, and it should involve significant political engagement and empowerment through co-learning. This assessment of participatory research in coastal fisheries also has significant implications for how we think of social capital and on how we may develop community-based resource management for a sustainable future.