Abstract:Depending on the bloom of Pseudonitzschia pungens in Gouqi Island in September, seven stations in four habitats around Gouqi Island were set up to analyze the community structure of phytoplankton. The abundance of phytoplankton in September is between 7.6 and 37.2 (×106/m3), Pseudonitzschia pungens dominated in the whole abundance which is 71.6 percent. Skeletonema costatum was one of the dominant species in the habitat of sandy beach compared with the small amount in other habitats. Combining with the environmental factors, the speciesenvironment matrix was established to do canonical correspondence analysis. The results showed that angle, ChlFlu, DO, salinity, P.quantum and temperature were the main factors affecting the structure of phytoplankton community (P<0.01). Skeletonema costatum was primarily influenced by temperature, so there was large abundance in the high temperature areas. According to the allyear data of species and environment, Pseudonitzschia pungens was primarily influenced by temperature.