Lake Taihu is a large shallow freshwater lake (surface area 2,338 km(2), mean depth 1.9 m) in China, which has experienced toxic cyanobacterial bloom dominated by Microcystis annually during the last few decades. In the present study, the dynamics of toxic and nontoxic Microcystis in three sampling stations (Meiliang Bay (site N2), Gonghu Bay (site N4), and the lake center area (site S4)) were quantified using quantitative real-time PCR (qPCR) during bloom periods from April to September, 2010. Our data showed that the abundance of toxic Microcystis and the toxic proportion gradually increased from April to August in water samples and reached the peak in August. During the study period, toxic Microcystis genotypes comprised between 26.2 and 64.3, between 4.4 and 22.1, and between 10.4 and 20.6 % of the total Microcystis populations in the three sampling sites, respectively. Correlation analysis suggested that there was a strong positive relationship between total Microcystis, toxic Microcystis and the toxic proportion. Chlorophyll a, total phosphorus, and water temperature were positively correlated with the abundances of total Microcystis and toxic Microcystis. Furthermore, the toxic proportion was positively correlated with total phosphorus (P < 0.05) and water temperature (P < 0.01), showing that global warming together with eutrophication could promote more frequent toxic blooms.