The reintroduction of a previously extirpated predator can engender conflict when the reintroduced species depletes customary fisheries to which indigenous communities have constitutionally protected rights. In the case of sea otter (Enhydra lutris) recovery on the west coast of North America, not only is Canada’s Species at Risk Act in conflict with Indigenous rights, but it also illuminates gaps in the principles of ecosystem-based management (EBM), such as equity and social justice. Broadly, we ask in this paper how EBM might be advanced if Indigenous communities were viewed as components of ecosystems having rights to a sustainable future equal to other components. Specifically, we explore evidence of sea otter management among precontact Northwest Coast societies and a contemporary co-managed system proposed by the Nuu-chah-nulth First Nations that would combine research with refinement of traditional hunting practices. We show that barriers persist through lack of knowledge of past controlled hunts, ignorance of recent experiences of successful community-based clam management, distrust of Indigenous capacity to self-manage or co-manage a hunt, and divergent values among actors.