The coral reef fisheries activity at the coastal area of Ternate Island may impact the coral reefs’ resources and ecosystems in this region. Management and utilization of the coral reef fishery resources that are not accompanied by an understanding of the structure and function of each component of the ecosystem can increase disturbance to the ecosystem, and adversely affect the structural components of the coral reef ecosystem in the coastal area of Ternate Island. Management and utilization of the coral reef fishery resources that are not accompanied by an understanding of the structure and function of each component of the ecosystem can increase the amount of disturbance to the ecosystem, and adversely affect the structural components of the coral reef ecosystem in the coastal area of Ternate Island. The lack of information and understanding of the ecosystem structure and function makes harvest controls impractical in fisheries management. Spatial management, such as MPAs, community marine tenure, and comprehensive marine zoning, within restrictions on destructive and inefficient fishing gear, may lead to reversing the decline in coral reef fisheries and the associated ecosystem. The urgent need to reform coral reef management focuses on the interconnected system as linked social-ecological systems.