Abstract: An integrated survey of the Yangtze Estuary was conducted in December 2016 to obtain the information of the phytoplankton groups and directed gradient analysis were carried out to explore the relationship between phytoplankton distribution and the environmental factors.96 and 63 phytoplankton species were identified during the neap tide period and spring tide period.Diatom, blue algae and green algae were the major phytoplankton group in survey area.Microcystis spp and Skeletonema costatum were the dominant species in the studied area.Based on the ecological characteristics and the distribution, the phytoplankton can be divided into four ecological groups:groups of freshwater, estuarine brackish water groups, nearshore low salt groups, ocean s groups.Margalef, Shannon-Wiener and Pielou's index were unevenly distributed in the study areas with high species diversity and evenness in Northeast areas.Canonical correspondence analysis (CCA) results of the relationship between phytoplankton species and environmental factors indicated that the salinity, conductivity, turbidity and nutrient salts jointly determined by the runoff of the Yangtze River and seawater determine the distribution of the phytoplankton in the Yangtze Estuary.