Dynamics of composition of different Microcystis spp. genotypes from June to November, 2008 in Meiliang Bay of LakeTaihu in China were investigated based on denaturing gradient gel electrophoresis analysis of PCR-amplified ITS (internaltranscribed spacer sequence) fragments. Simultaneously, we investigated the relative abundance of microcystin-producingMicrocystis spp. (the ratio of the toxic Microcystis to total Microcystis) based on microcystin synthetase gene (mcyA) and partialMicrocystis-specific 16S rDNA sequence using real-time PCR. The results of this study indicated that there were shifts ofcomposition of different Microcystis genotypes during algae bloom in Lake Taihu. The most abundant genotypes were found in thelate of August, September and October. Genotypes M5 and M10 were found every month. A total of twelve main genotypes werefound, and the relative abundance of each genotype changed during the development of algae bloom. Quantitative real-time PCR(qRT-PCR) revealed that the abundance of toxic Microcystis increased from 0.75% to 32.16% from June to October and decreasedsignificantly in November.