Marine protected areas (MPAs) are an increasingly popular tool for management of the marine commons. Effective governance is essential if MPAs are to achieve their objectives, yet many MPAs face conflicts and governance challenges, including lack of trust and knowledge integration between fishers, scientists, and policy makers. This paper considers the role of a boundary organization in facilitating knowledge integration in a co-managed MPA, the Gladden Spit and Silk Cayes Marine Reserve in Belize. Boundary organizations can play an important role in resource management, by bridging the science-policy divide, facilitating knowledge integration, and enabling communication in conditions of uncertainty. Drawing on ethnographic research conducted in Belize, the paper identifies four challenges for knowledge integration. First, actors have divergent perspectives on whether and how knowledge is being integrated. Second, actors disagree on resource conditions within the MPA and how these should be understood. Third, in order to maintain accountability with multiple actors, including fishers, government, and funders, the boundary organization has promoted the importance of different types of knowledge for different purposes (science and fishers' knowledge), rather than the integration of these. Finally, a lack of trust and uneven power relations make it difficult to separate knowledge claims from political claims. However, even if knowledge integration proves difficult, boundary organizations may still play an important role by maintaining accountability, providing space for conflicting understandings to co-exist, and ultimately for governance institutions to evolve.