Water quality variables and phytoplankton in Shanzi Reservoir in Fujian Province were monitored and sampled during aperiod of the summer stratification. The fluorometry and light microscopy were used to measure the phytoplankton abundance andthe biomass of phytoplankton in water column and sediment.The results showed that a clear thern}al stratification was formed insummer and could cause the stratification of the physical and chemical parameters. Microcystis, the absolutely dominant Cyanophytaspecie in Shanzi Reservoir, had a higher abundance in surface water than in bottom, and the biomass presented a sharp declinebellow the thermocline. Hence, the thermal stratification might affect the vertical distribution of phytoplankton population. Theabundant cyanobacterial cells in sediment could provide a "species of source" for water blooming in summer.