Phytoplankton communities in the Yangtze River estuary were studied by cluster analysis based on the samples collected in August 2003,in the cruise for Yangtze River estuary deepwater channel.50 phytoplankton species were identified and grouped into three ecotypes: the estuarine community,the dilute community and the high salinity community.The estuarine species are the main part of phytoplankton community,which dominates the community feature of Yangtze River estuary.The 20 stations can be separated into three groups(named group I,II,III) by the cluster analysis based on the species composition.Group I was in the west area of the Changxing Island,group II and group III were in the east area of the Changxing Island.According to the environmental factors in which species distributed,salinity,turbidity and suspended sediment were different significantly with each other.