Abstract:The distribution of cyanobacteria and microcystin in two pumped storage reservoirs, Fenghuangshan Reservoir and Nanping Reservoir in Guangdong Province was bimonthly investigated in 2008. Forteen genera were identified, and most of them were filamentous and colonial ones, such as Pseudanabaena, Limnothrix, Dactylococcopsis, Cylindrospermopsis and Chroococcus. Cyanobacteria abundance in two reservoirs ranged from 119 to 137373 cells mL-1, and microcystin concentration from 0 to 2.26 μg L-1. In Fenghuangshan Reservoir with relatively long retention time (160 d), microcystin concentration was lower than the national standard for drinking water of 1 μg L-1 throughout the year, which the maximum was in March. In the short retention time (60 d) reservoir, Nanping Reservoir, the concentration of microcystin was higher than that in Fenghuangshan reservoir in the flood season with the maximum in July. In Fenghuangshan Reservoir, the abundance of cyanobacteria was one order higher than that in Nanping reservoir. Maximal abundance occurred in dry season (March) in both the reservoirs, and nutrient loading related to pumping strategy and temperature were two possible factors in seasonal variation of cyanobacteria abundance. In Fenghuangshan Reservoir, Pseudanabaena, Limnothrix and Cylindrospermopsis were dominant in cyanobacteria and contributed more than 50% of the total abundance at most of time. In Nanping Reservoir, cyanobacteria was dominated by filamentous species in dry season and by colonial species in flood season. The temperature and nutrient loading related to pumping strategy seemed to key factors inducing cyanobacteria seasonally dominated by different ecotypes of species in Nanping Reservoir.