Dynamics of Synechococcus (Syn), Prochlorococcus (Pro) and picoeukaryotes (Euk) was studied at 92 stations in the Pearl River Estuary and adjacent shelf waters in the winter of 2006 using flow cytometry. The average cell abundance of photosynthetic picoplankon (Pico) was 104 cells/ml. Picoeukaryotes was the dominant group in the inner estuary where Pro was absent. Synechococcus was dominant in the coastal and open waters. The proportion of Pro was higher in the open than in the coastal waters. The change of Pico community structure from the inner estuary to the open waters is related to the changes in hydrochemical dynamics. The vertical variations in the abundance and community composition of Pico were not significant. The abundances of Pro and Syn were positively correlated with temperature, salinity and pH, whereas they were negatively correlated with dissolved oxygen (DO), suspended sediment concentrations (SSC) and nutrients (nitrogen, phosphorus and silicon) concentrations. But the correlations between %Euk (as of total pico) and these environmental factors were opposite to those between the abundance of prokaryotic cells (Pro and Syn) and the environmental factors. %Euk had significant negative correlations with temperature, salinity and pH, and positive correlations with DO, SSC and nutrients. There were differences in the niches between prokaryotic cells and picoeukaryotes. Prochlorococcus and Syn were dominant in the warm waters with high salinity, low SSC and low nutrient concentrations, while %Euk was higher in the cold waters with low salinity, high SSC and high nutrient concentrations. Results of principal component analysis and regression analysis indicated that the relationship between the abundances of Pico and the environmental factors was a compound function (y = b0(b1)x), and that between the abundances of Pro, Syn or %Euk and the environmental factors was a linear function.