With the rapid development of the coastal environment and advances in fishing technology, marine biodiversity and fishery resources are decreasing dramatically. Therefore, each state is now focusing on conserving the marine environment. Planning Marine Protected Areas is one of the simplest and most efficient ways to do this. In recent years, researches have been conducted on Marine Protected Areas around the world. The government and academic fields in Taiwan also has started to value its surrounding marine environment. However, literature on the Marine Protected Areas in Taiwan has focused on policy and management, not so much on planning and zoning strategies. Therefore, this study uses the Geographic Information System (GIS) to simulate the planning and zoning process. This research set principles and zoning framework for Marine Protected Areas in Taiwan based on case studies and spatial analysis techniques. This study uses Gueishan Island in Yilan County as case study since the unique geographical environment of Gueishan Island provides potentiality to set Marine Protected Areas. In this study, it is suggested that "hot spring resources", "cetacean resources", and "fisheries resources" are the main protected objectives. The zoning strategies, management guidelines and recommendations are provided in this study based on these three protected objectives. According to the GIS simulation process, using the spatial analysis techniques is one of the possible efficient methodologies to plan and zone the Marine Protected Areas. With supplementary data and information, the results can be discussed more specifically in the further study. In addition, techniques of visualization during the MPAs zoning process can be a easier way for various stakeholders to understand, and to strengthen mutual communication, thereby reducing disputes to create successful Marine Protected Areas.