Abstract:The seasonal fluctuation of cyanobacteria population in the through-flowing reservoirs of Shenzhen and Feilaixia in Guangdong Province was investigated in 2004. Seventeen genera of cyanobacteria composed mainly of filamentous ones were obtained. The common genera were Pseudanabaena, Microcystis and Dactylococcopsis. Cyanobacteria density ranged from 5 to 2 052 cells ml-1. The maximum cell density was found in Shenzhen Reservoir in June with filamentous species abundance of over 75%. The peak of cyanobacteria abundance was present in Feilaixia Reservoir in December with filamentous species occupying 90%. Cyanobacteria abundance and composition were changed mainly by hydraulic condition. The seasonal fluctuation of cyanobacteria population was more affected in Feilaixia Reservoir than in Shenzhen Reservoir since the hydraulic retention time of Feilaixia Reservoir had a greater variation than that of Shenzhen Reservoir. Filamentous cyanobacterias, especially Pseudanabaena, adapt to the reservoirs better than the other cyanobacteria species under high levels of nitrogen and phosphorus conditions. And their abundances will greatly increase when the retention time is prolonged.