This paper reports on the phytoplankton community, its composition, structure and distribution in Changjiang estuary from February 1999 to March 2000. Two hundred and eight species were identified in the dry and flood periods. Diatoms, with 143 species observed, was the most abundant phytoplankton group, accounting for 68.75% of the total phytoplankton species number. Skeletonema costatum was dominant among all the species. The phytoplankton of Changjiang estuary in China was divided into five ecological categories: freshwater species, estuary brackish water species, inshore low salinity species, inshore widespread species and off-sea high salinity species. During the dry period, the major phytoplankton populations in the surface layer were estuary inshore and offshore populations, distinguished from the composition of the bottom layer. The community structure was similar in the two layers during the flood period. The phytoplankton species diversity was calculated for Simpson, Shannon–Weaver diversity and evenness indices, and found to be higher in the dry period, due to the simple dominant species and low spatial heterogeneity in the flood period. Higher phytoplankton abundance was observed in the surface layer during the flood period. The phytoplankton species distribution, coinciding with the dominant species distribution, varied with salinity, and their abundance correlated significantly with nutrients and light.