While the participatory management of small scale fisheries has been widely promoted, we have limited understanding of the factors influencing its effectiveness. Here, we highlight lessons learnt from the implementation of Madagascar’s first locally managed marine area (LMMA), drawing on our insights and experiences as staff of a comanaging nongovernmental organization (NGO). We describe the LMMA’s context and history, and highlight aspects of our approach that we feel underpin its outcomes, including: (a) comanagement rather than community‐management; (b) the permanent field presence of a supporting NGO; (c) a management focus on locally important natural resources; (d) the implementation of poverty alleviation initiatives aimed at reducing barriers to management; (e) decision‐making by resource users rather than scientists; (f) a diversified, entrepreneurial funding model; and (g) an emphasis on monitoring and adaptive management. We also highlight several challenges, including: (a) the inability to influence fishery supply chains; (b) promoting participation and good governance; (c) promoting rule application; (d) standing up to outsiders; (e) promoting environmental management in the long term; and (f) maintaining funding. Our experiences suggest that small scale fishers can be effective natural resource managers in low‐income contexts, but may need extended support from outsiders; however, the role of supporting NGO is nuanced and complex.