The dispute over the establishment of Marine Protected Areas (MPAs) continues to occur along with the increasing efforts to conserve marine resources. Efforts to reduce disputes have become a prominent issue since it will affect efforts to protect and preserve marine ecosystems. The main challenges in establishing MPAs in Taiwan are political issues, lack of engagement, and differences in understanding among stakeholders. The purpose of this study is to analyze disputes over the establishment of MPAs in Taiwan, then provide solutions to the settlement. The data was collected using two methods, namely the collection of documents and interviews with staff and officials at the Marine National Park Headquarters, Construction and Planning Agency, Taiwan. This study analyzes and interprets all data qualitatively. The result is that political competition between the central and regional governments has disrupted cross-level coordination to implement ecosystem protection and conservation through the establishment of MPAs. The political intervention also influences the decision-making process for the establishment of the MPAs, and this increases dispute tension. Therefore, it requires the legitimate engagement of stakeholders through a bottom-up approach. Legitimate engagement can facilitate the ideas and aspirations of stakeholders, and this is useful for realizing the consensus. Furthermore, misunderstanding caused by differences in knowledge can lead to disputes. Appropriate information management is required through sharing and exchanging information to overcome this misunderstanding.