The Java Sea is a major fishing ground in Indonesia contributing 31% of the national marine fisheries production. Demersal and small pelagic fishery resources account for most production in the area. During the 1960s and 1970s, strong demand for fish, which in Indonesia resulted from both increased human population and increased per capita fish consumption, stimulated the development of fishing in the Java Sea. This led to development of up-stream and down-stream industries, increases in employment opportunities, and increases in the number of fishers and fishing households. Like most Indonesian fisheries, the Java Sea fisheries may be characterized as de facto open access with no restrictions on fishing effort. Free competition occurs among large-scale and small scale fishers. Increasing numbers and sizes of fishing gear and boats, as well as extension of operations into new fishing grounds, have resulted in biological and economic over-exploitation. Meanwhile, the quality of coastal habitats such as mangroves and coral reefs has decreased due to adverse effects of human activities. Over-exploitation, as indicated by decreases in CPUE and profit per vessel, and environmental degradation has led to poverty of fishers in coastal areas. Small scale fishers who comprise the majority of fishers have suffered most because the small boats they operate are less efficient. Fisheries management in the Java Sea would involve controlling fishing effort, which in turn would require the provision of alternative livelihood for displaced fishers. This paper describes key features of an “Integrated Program of Fisheries Management and Development for the Java Sea”, and outlines the activities for improving fisheries management in the area. Among other things, the program calls for establishment of a Fisheries Management Body to implement management at a regional level with the central government supervising the provincial governments. All stakeholders should be involved in managing the fisheries. Beyond the Java Sea fisheries, two actions are recommended to promote regional co-operation and sharing of experiences with other countries. These are (1) networking for transfer of information and experiences on fisheries co-management, and (2) regional pilot projects for shared stock management.