The amount of Microsystis cells at the entrance of rivers to southern Lake Taihu has important influence on the drinking water security and water quality to county nearby and Lake Taihu.A real-time fluorescence quantitative PCR method was established using the microcystin synthetase gene mcyE/ndaF as target in this study.The quantity of Microsystis cells at the entrance of rivers to southern Lake Taihu was assayed.Results showed that the specificity, accuracy and repetitiveness of the method were good.The standard curve to detect Microcystis aeruginosa was y=-3.454x+49.88.The slope, correlation coefficient and amplication efficiency were -3.454, 0.991 and 94.6%, respectively.It was revealed that the amount of microcystin producing blue-green algae at site of Jiapu and Hexi was the highest among the 7 sampling sites, reaching (1.99±0.35)×10⁵ and (1.47±0.23)×10⁵ cells/ml, respectively.The main microcystin producing species was Microcystis aeruginosa in all the sampling sites.This method could be used rapidly and accurately to detect the quantity and type of the microcystin producing blue-green algae, and provide evidence for algal bloom and early warning.