This paper reports on a project to engage researchers and fishers together in adapting 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). Its rationale reflects arguments that (1) effective community-based management requires that managers are able to pose and address social science questions, (2) participatory research, involving true cooperation in all stages, can support this process, and (3) there is a need to overcome practical and methodological barriers faced in developing participatory research protocols, to serve the needs of community-based management while not demanding excessive transaction costs. In this paper, we report on work with fisher organizations, both aboriginal and non-aboriginal, in which social science priorities were set by each organization, and small-scale research projects designed and carried out to meet these needs. This work identified interests among fishers in research on three different levels of meaning: (1) practical livelihood concerns, including what, when and where to fish, and with what intensity of effort, (2) social, economic and political issues (e.g., on institutional structures, politics of access and allocation, overlap and conflict between regulatory regimes), and (3) values and ethics that implicitly or explicitly guide policy development and implementation. Several research themes proved crucial, including those of power sharing, defining boundaries of a community-based group, access and equity, designing effective management plans, enforcement, and scaling up for effective regional and ecosystem-wide management. The research results demonstrate the effectiveness of extending participatory methods to challenge traditional scientific notions of the research process.