Penghu archipelagoes possess long seashore lines, rich marine fauna and flora. The marine environment around Penghu is mainly affected by the South China Sea Current, China Coastal current and Kuroshio Cuurent. Previous studies on the marine biodiversity in Penghu mostly focused on the species lists. Information about the other important parameters of biodiversity such as abundances and distributions was few. The aim of this project is to integrate those with Geographic Information System (GIS) to provide useful references for reservations and further sustainable utilization in Penghu. Clustering analysis of species abundance of surveyed sites shows that east and north sections group together and the south section is independent one. Further multiple dimensional scaling (MDS) and analysis of similarity (ANOSIM) also support the former results. According to the previous results of past three years, there are 18 genera, 40 species of Scleractinian coral in north/east sections, 18 genera, 62 species in south section and 18 genera, 38 species in inner section around Penghu water. As for the crustacean, there are 37 genera, 56 species in east secton, 23 genera, 39 species in north section, 56 genera, 89 species in south section and 25 genera, 36 species in inner section. Concerning the macroalgae, there are 56 genera, 90 species of Scleractinian coral in north/east sections, 63 genera, 99 species in south section and 60 genera, 100 species in inner sections around Penghu water.