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The 1982 United Nations Convention on the Law of the Sea (UNCLOS) requires coastal states of semi-enclosed seas, like the South China Sea (SCS), to coordinate in the management and conservation of marine environments and living resources, specifically highly migratory trans-national stocks. One of the world’s top five fishing grounds, sovereignty disputes continue to bedevil joint fisheries management in the SCS. To develop new norms and standards for regional cooperation, and to support parallel domestic fisheries policymaking, scientists from China, Indonesia, Malaysia, the Philippines and Vietnam overcame political constraints and data limitations, to develop a Common Fisheries Resource Analysis (CFRA) of skipjack tuna (SKJ). A valuable highly migratory species SKJ is fished extensively by SCS states, but regionally, was previously, unassessed. Applying Length- Based Spawning Potential Ratio assessment to evaluate catch size compositions within a Weight of Evidence framework, we conclude fishing targeted at adult stocks would probably be sustainable, but for the continuing intensification of fishing for juveniles. Fishing pressure is apparently eroding SCS food webs and serially depleting local stocks. We conclude, domestic policies need to be developed to halt the continuing expansion of fishing fleets, and reduce fishing pressure, particularly on juvenile fish. The challenge of policy development and implementation requires the support of international frameworks, like Regional Fisheries Management Organisations (RFMOs), to regularise cooperation between government and non-government scientists of coastal states The existing Western Central Pacific Fisheries Commission (WCPFC) could provide that framework, unfortunately, intensifying geopolitical competition makes that extremely unlikely.