There has been a gradual evolution in fisheries management over the past decades from a focus on sustainability of a single species or stock and resources to a focus on marine ecosystems. Among the issues to be addressed for effective implementation of ecosystem based fisheries management(EBFM) are the appropriate governance arrangements and scale for management. The purpose of this paper is to examine these issues of governance and scale as related to EBFM in tropical developing countries through an analysis of approaches being taken in the Philippines to manage fisheries on a multi-jurisdictional level. The management of fisheries and coastal resources in a number of bays and gulfs, which represent marine ecosystems, is presented.The opportunities and constraints to ecosystem based fisheries management in the Philippines are discussed and lessons for broader application of these governance structures in tropical developing country marine ecosystems are presented.