Abstract: Three cruises were conducted in the Yangtze River estuary from April to November in 2009. The density and composition of phytoplankton were determined in water samples collected at thirty sampling sites. Totally 8phyla, 95genera and 330species were identified in these samples. Diatoms and dinoflagellates, especially Skeletonema costatum, were the dominant species at most sites. The abundance of phytoplankton in seawater decreased with the increase of distance from Yangtze River and a bloom was observed in the summer of 2009. By calculating the diversity index (H), Yangtze River transition water has the largest phytoplankton diversity. The maximum value of H in the sampling area occurred in November. Phytoplankton in the estuary of Yangtze River could be divided into four groups and a significant difference of phytoplankton composition was observed in three sampling seasons. CCA ordination analysis indicated that environmental factors play important roles in controlling the phytoplankton community structure, while the controlling factors vary with seasons. The primary factors affecting the structure of diatom community were identified to be COD_Mn and NO₃^--N content in April, to be SiO₄^4--Si, NO₃^--N and PO₄^3--P content in August, and to be PO₄^3--P and SiO₄^4--Si in November. Contents of NH₄⁺-N, COD_Mn, and NO₃^--N and the transparency were the main factors affecting the structure of dinoflagellates in April, August and November, respectively. These results indicated that environmental factors play important roles in the seasonal and spatial variations of phytoplankton community structure in Yangtze River estuary, and the major driving factors changed with seasonal changes.