Investigations of phytoplankton community characteristics in the surface and bottom layers of the Dogai Coring Lake were conducted from April 27 to May 6 in 2009. Fifty-eight sampling stations covered the whole lake. Differences in phytoplankton species composition, density, biomass, diversity and distribution of different latitudes or longitudes in the surface and bottom layers of the Dogai Coring Lake were analyzed. The results showed that a total of 121 species of phytoplankton were identified in the surface layer,the dominant species are Nitzschia sp. and Navicula sp.; 189 species in the bottom layer, the dominant species are Nitzschia sp., Navicula sp., Hantzschia sp. and Hantzschia amphioxys. Bacillariophyta is dominant in species numbers by over 60%. The species between the surface and bottom layers are medium dissimilarity. Higher density (68.434×10⁴ cell/L) and biomass (0.819 8 mg/L) of phytoplankton in the bottom layer than the density (8.444×10⁴ cell/L) and biomass (0.102 1 mg/L) in the surface layer, but the phytoplankton diversity index in the bottom layer is lower than the surface. There was a significant difference between the surface layer and the bottom layer (P < 0.05). The results of cluster analysis revealed the structure in the bottom is more simple than that in the surface, but distribution on the different latitudes or longitudes is similar.