A preliminary study was conducted on the phytoplankton community structure and the annual variation of species diversity in Mingzhu Lake of Chongming Island from January to December 2007. A total of 120 phytoplankton species belonging to 8 phyla and 63 genera were collected, among which, Phormidium tenue, Meismopedia tenuissima, M. convoluta, Microcystis incerta and Synedra ulna were the dominant species. The mean annual density and biomass of the phytoplankton were 5361.57 x 10(4) cell x L(-1) and 7.68 mg x L(-1) respectively. There was a significant difference in the monthly phytoplankton standing crop (P < 0.01) , being the highest in July, but no significant difference was observed among different observation stations. The Shannon index and Margalef index of the phytoplankton community were higher in spring and winter than in the summer and autumn. Biological evaluation indicated that the water quality of Mingzhu Lake was better in spring and winter than in the other two seasons, and canonical correlation analysis (CCA) suggested that the main factors affecting the phytoplankton community were water temperature, followed by total phosphorus, and total nitrogen.