Abstract: Based on the four phytoplankton survey date in November 2013, May 2014, February and August 2015 in Hengqin island sea area, the species composition, spatial and temporal distribution and diversity of phytoplankton were analyzed.Results showed that a total of 140 phytoplankton species were identified in four phylum.101 species of Bacillariophyta, accounting for 72.14%; 33 species of Pyrrophyta, accounting for 23.58%; 3 species of Chlorophyta, accounting for 2.14%; 3 species of Cyanophyta, accounting for 2.14%.There were 64 species in autumn, 52 species in spring and winter, 36 species in summer.The annual abundance of phytoplankton ranged from 2.7×10⁴ to 20100.40×10⁴ ind/m³, averaged 1613.43×10⁴ ind/m³.The dominant species of spring and summer were less, the dominant species were more in autumn and winter.The dominant species was only Skeletonema costatum in spring, Skeletonema costatum and Ditylum brightwellii were appearing in summer, Skeletonema costatum, Coscinodiscus centralis and Coscinodiscus jonesianus were appearing in autumn, while Thalassiosira subtilis and Chaetoceros densus seven kinds were appearing in winter.Shannon-Wiener diversity index (H'), Pielou evenness index (J'), Diversity threshold (Dv) and Margalef richness index (D) were 2.52, 0.63, 1.67, 0.80 in winter; were 2.46, 0.63, 1.64, 0.80 in autumn; were 1.78, 0.52, 0.98, 0.53 in summer; and were 0.27, 0.11, 0.10, 0.32 in spring.While four index were very low in spring, indicated that the community characteristics was unusual, and the ecological environment has been a certain degree of pollution and damage.There was no significant correlation between phytoplankton abundance and environmental factors in spring.Phytoplankton abundance was significantly positively correlated with pH (P < 0.01) in summer, and negatively correlated with active phosphate (P < 0.05).Phytoplankton abundance was positively correlated with inorganic nitrogen (P < 0.05) in autumn.In winter, phytoplankton abundance was positively correlated with salinity (P < 0.05), but significantly negatively correlated with inorganic nitrogen (P < 0.01), and negatively correlated with water temperature (P < 0.05) and active phosphate (P < 0.05).