The grazing effects of two cladoceran species (Daphnia magna and D. carinata) on the community structure of phytoplankton of Lake Dishui in Shanghai was studied in September 2012. The results showed the concentration of NH+ 4-N, soluble reactive phosphorus (SRP) and chlorophyll-a obviously increased comparing with the control. In the group of D. magna and D. carinata, the concentration of NH+ 4-N increased 2.26-fold and 3.82-fold respectively, the concentration of SRP increased 3.41 times and 3.32 times respectively, the concentration of chlorophyll-a decreased 80.4% and 75.2% respectively. Meantime, the concentrations of NH+ 4-N and SRP showed a significant relationship with chlorophyll-a in the Daphnia treatment. The community structure of phytoplankton significantly changed when the Daphnia were added. The density of phytoplankton decreased 70.3% and 80.0% when D. magna and D. carinata were added respectively. The density of Chlorophyta , Cyanophyta and Bacillaripohyta decreased 69.61%, 64.78% and 31.38% respectively in D. magna treatment. The density of Chlorophyta , Cyanophyta and Bacillaripohyta decreased 96.41%, 62.65% and 66.84% respectively in D. carinata treatment. The Cryptophyta, Euglenophyta and Pyrrophyta were not found at the end of experimentation. The experiments showed D. magna and D. carinata can efficiently control the density and change the community structure of phytoplankton. At the same time the density of periphyton obviously decreased, which showed that D. magna and D. carinata can graze the periphyton.