A cruise was conducted from late August to early September 2004 with the intention of obtaining an interdisciplinary understanding of the Yangtze River Estuary including the biological, chemical and physical subjects. Water sample analysis indicated that total phytoplankton species richness was 137. Of them 81 were found in Bacillariophyta and 48 in Pyrrophyta, accounting for 59.1% and 35.0% respectively. The average cell abundance of surface water samples was 8.8 ×104 cells L-1, with the maximum, 102.9 × 104 cells L- 1, encountered in the area (31.75°N, 122.33°E) and the minimum, 0.2× 104 cells L-1, in (30.75°N, 122.17°E). The dominant species at most stations were Skeletonema costatum and Proboscia alata f. gracillima with the dominance of 0.35 and 0.27. Vertical distribution analysis indicated that obvious stratification of cell abundance and dominant species was found in the representative stations of 5, 18 and 33. Shannon-Wiener index and evenness of phytoplankton assemblage presented negative correlation with the cell abundance, with the optimum appearing in (30.75°N, 122.67°E). According to the PCA analysis of the environmental variables, elevated nutrients of nitrate, silicate and phosphate through river discharge were mainly responsible for the phytoplankton bloom in this area.