A preliminary study was conducted on the community structure of phytoplankton and the annual variation of species diversity quarterly from October 2010 to July 2011 at the 18 stations in the Jiuduansha inshore waters of the Yangtze River estuary. A total of 133 phytoplankton species were identified, which belonged to 55 genera of 6 phyla. Diatom was the major phytoplankton group and its species number accounted for 61.65% of all species. The annually average cell abundance of phytoplankton was (92.33±29.86) ×104cell?L-1.The phytoplankton, according to its ecotype and habitat, can be grouped into freshwater, coastal and eurysalinity and oceanic species. The main dominant species was Skeletonema costatum, of which average cell abundance was (87.95±30.96) ×104cell?L-1. It was the absolute superiority in cell abundance and frequency occurrence of Skeletonema costatum that resulted in the prominence of the single dominant species, lower diversity, uneven distribution and community simplification of the waters.