Community-based coastal resource management (CBCRM) is a scheme that gives a community a certain degree of management responsibility, such as the ability to supervise access and use of the coastal resource.  The Fisheries Sector Program (FSP) is one of the government-initiated CBCRM programs intended to augment the income of small-scale fishermen and preserve the coastal resource.  However, despite the numerous studies carried out relating to CBCRM programs, none dealt with the transaction costs (TC) associated with their implementation. This study generally aims to estimate and analyze the TC associated with the implementation of a multi-level and multi-stakeholder program such as a CBCRM program. TC are indirect costs incurred in reaching and enforcing agreements. Tools for analysis used in this study included the estimation of direct project costs (DPC) and TC at each phase of the San Miguel Bay Coastal Resource Management Program (SMB-CRMP) and their distribution among the different stakeholders; determination of transaction costs share (TSC) and analysis of factors affecting TC. Similarly, effect of TC on performance of people's organizations (POs) was analyzed.