Abstract There are three marine protected or conservation areas (MPA or MCA) at Southern Taiwan that are enriched with marine resources. These sites are assigned by the order of government administration. The Kenting National Park was first established in 1984. In 1987, the Executive Yuan also passed two more coastal sites, Jien-sen and Jiou-peng, as marine protected areas. The government has adopted the strategy and policy on the marine coastal sites but it has lack of clarity on the administration and authority to manage the site since their establishment. The local residences also are not pleased with the site selection for setting up the marine protected area because of the problems of economic need and their livelihood influences from the protected site restrictions. These have caused the inefficiency of implementation on the management of the marine protected sites to protect and conserve the marine resources.The present studies research to understand both the Houbihood pilot protected site in Kenting National Park and the Jen-sen coastal protected area for a better operation mechanism with regard to managing the conservation sites. The research employs the literature search, interview to local residences and scientists to obtain information about the operation and management of marine protected site. These include the issues of site establishment, zoning and process, law requirement and implementation, public inquiry and participation, committee organization and site management. The obtained survey results were made to compare with the successful management scheme and organization of the Basin Head marine conservation site, Prince Edward Island Province of Canada. The Basin Head Conservation Committee serves a good example for setting up marine conservation areas in Southern Taiwan. The establishment of marine protected area requires background data information including the law and policy, organization structure, manpower and resources for the justification of implementation and its operation in order to achieving the protection and conservation at the marine environment. The present studies report that the government administration must have a unique guidelines and criteria for the national use as well the local application. The government shall draw a long term planning and strategy for law enforcement and practical cooperation scheme between the government, local organization including non-government organization and the assistance of Taiwan Coastguard Administration. The fundamental issues include the survey and collection of background data for the environmental and ecological data information at the marine protected site.