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Since the 1990s, the Ecosystem Approach to Fisheries (EAF) has developed rapidly and become an important method of high seas fishery management. The EAF has already been practiced by many Regional Fisheries Management Organizations. The practice of the approach in the management of high seas fisheries faces numerous challenges, such as constraints by the approach, increasing stakeholders affecting the implementation of the EAF, inconsistency with political ocean boundaries, resistance from vested interests, and the threat of Illegal, Unreported, Unregulated fishing. In order to deal with the dilemma faced by EAF, ideas are proposed as follows, building a sense of maritime community with a shared future, advancing the approach by explicating definition, objectives, and priorities, strengthening coordination and cooperation between the states and regional fisheries organizations, adopting area-based management tools with biogeographical criteria, and enhancing the level of stakeholders’ participation.