Phytoplankton samples of the Sanjiang Plain Wetland (Fuyuan region) were collected from 10 sampling sites in June 2012. A total of 262 taxa belonging to 7 phyla, 9 classes, 22 orders, 32 families, 73 genera, 239 species, 19 varieties and 4 forms were identified. Chlorophyta, Bacillariophyta and Euglenophyta dominated the phytoplankton community, were 42.6%, 22.8% and 20.9%, respectively. The total cell density at different sampling sites varied from 3.88×10⁴-278.07×10⁴ cells/L. The results of cluster analysis divided the 10 sampling sites into two regions:farm region and non-farm region, and the differences in phytoplankton communities of these two regions were significant. The Shannon-Wiener diversity indices were about 2, Margelef indices were above 3, and Pielou evenness indices ranged from 0.3-0.5. Phytoplankton compositions in the farm region were more complex than those in non-farm region. Based on the species composition and diversities, it was suggested that the phytoplankton diversity of the Sanjiang Plain Wetland (Fuyuan region) was good and appropriate for the growth of the phytoplankton.