This dissertation uses ¡§marine good governance¡¨ as the core to discuss the establishment of marine protected areas institutions in Taiwan. As a marine nation, it is a fatal key whether Taiwan can properly manage marine resources or not. Appropriately dealing with marine-related affairs can bring success to overall national development. The marine environmental diversity makes its affairs much more complicated than the land area. The global cognition of marine management has greatly changed. ¡§The concept of public management¡¨ has shifted from ¡§government¡¨ to ¡§governance¡¨. Good governance is the aim of public management nowadays. A marine nation should aim to have good marine governance. Establishing integrated marine institutions would be the key point. Although the quantity of Taiwan¡¦s marine protected areas has greatly increased, the effectiveness of management on marine protected areas is still called into question. This dissertation recommends that Taiwan should focus on integrating the institutions on marine protected areas. The future Marine Affair Organization and the corresponding marine governance legal structure would result in a ¡§Good Governance of a Marine Nation¡¨.