The protection and biodiversity of marine ecosystem become major concerns in the world. Taiwan is also increasingly interested in the establishment of marine protected areas, but it still lack of the scheme on ¡§how to perceive the process for the protected areas¡¨. The establishment of a protected area is all by the top down without a full planning for a proper managed mechanism, evaluation and assessment to the site. The lack of the funds from the government often causes the failure of monitoring and restoration to the protected site. These problems have caused unprovent from imappropiate management to the established protected areas or have made the protected site as a paper park by the administration. This study searches the literatures with regards to the planning processes and the site selection process of marine protected areas in Canada and Australia. The objective of the present study is initiated to determine and survey the problems of marine protected area (MPA) planning in Taiwan. The select sites for the present studies are the proposed MPA site ¡§Four Southern Island¡¨ and other established MPA sites in Penhu. The approaches for assessing the sites include the geographic information system (GIS) spatial analysis method for the aquatic resources and their distributions. Data collections consist of the funding sources for managing the MPA sites and the proposed planning for the delimitation of MPA at the shore areas. The biological information around the sites was assessable for the evaluation process in addition to the management scheme in the future requirement at the Four Southern Islands site. The current expanses supported by the Penhu county government and the Executive Yuan Coast Guard was used for comparing with the proposed budgets needed for the MPA sites. The results showed that the Four Southern Islands has not met with the requirements and guidelines as a MPA due to the lack of scientific survey on the distributions of aquatic species within the proposed 3 nm delimitation. A long-term research and monitoring of the resources shall be performed to evaluate the sites prior to be announced as a designate MPA site. Although local residents agreed positively about the important of MPA site establishment through the questionnaire and interviews, there is still the need to improve management practices and more strict law enforcement capacity to ensure the protection of the marine environment for achieving a sustainable development. The survey results have been made to the process of site selection of marine protected areas according to Canada, suggesting that the current planning of the Four Southern Islands in Penghu does not match the site selection process. There need to be clarified with the details of the implementation process. In the end, above finding may impact the establishment of protected areas, including the relationship between public sector¡¦s responsibilities, and socio-economic conditions of the surrounding area development, marine environment and resources and fishing activities and other aspects of the integration considerations. These are expected to be the important conditions for the recommendations for the MPA site selection and to ensure the sustainable development of marine environment.