The focus of this paper is on the governance of small-scale or municipal fisheries in the Philippines in light of the critical role they play in the livelihoods of coastal communities and in the nation as a whole. The information and insights presented in this lessons learned brief derive from the project entitled Strengthening Governance and Sustainability of Small-Scale Fisheries Management in the Philippines: An Ecosystem Approach. The project was funded principally by the Department of Agriculture's Bureau of Agricultural Research (DA-BAR), and implemented from 2008 to 2011 by WorldFish in collaboration with the Department of Science and Technology (DOST) and selected partners. The underlying project's goal was to 'strengthen governance and sustainability of small-scale fisheries management in the Philippines.' There were a variety of objectives spread across two project phases but the primary objectives relevant to this brief include: (1) identifying issues at project sites and assessing potential for an ecosystem based approach to fisheries management, and (2) assessing current fisheries management practices at different levels of governance and identifying best practices. The purposes of this paper are twofold. First, it aims to provide brief highlights of the project findings; second, it aims to present the lessons learned in project implementation covering substantive sectoral concerns as well as methodological issues. It wraps up with some strategic directions that need to be undertaken to reverse the deteriorating conditions of small-scale fisheries (SSF) while at the same time promoting their sustainable development.