Participatory diagnosis is an approach to identify, prioritize and mobilise around factors that constrain or enable effective governance and management in small-scale fisheries. Diagnostic frameworks are mostly designed and used for systematic scientific analysis or impact evaluation. Through participation they also have potential to guide contextually informed improvements to management in practice, including transitions to contemporary forms of governance like the ecosystem approach to fisheries (EAF). In this paper, the authors demonstrate different ways to undertake a participatory diagnosis of the potential for governance transitions, and they analyze the challenges and opportunities identified during this phase of the transition to EAF in small-scale fisheries in Indonesia, Philippines, Solomon Islands and Tanzania.