Lake Taihu is a large, shallow, eutrophic freshwater lake, which has frequently experienced cyanobacterial bloom in summer in the past decades. In winter, a large quantity of cyanobacterial cells sink on the sediment surface to overwinter. Therefore, it is important to quantify the biomass of cyanobacteria on the sediment to predict the location and the extent of water bloom in summer. However it is difficult to identify and to count cyanobacterial cells in sediment using microscopy method, and microscopic identification cannot differentiate between the toxigenic and non-toxigenic genotypes. In recent years, this problem has been resolved by using molecular techniques such as PCR and quantitative real-time PCR (qPCR) with primers targeting toxin-producing genes. The microcystin gene cluster which contains 10 genes, namely from mcyA to mcyJ has been widely used to reveal microcystin-producing species in genera Anabaena, Microcystis and Planktothrix. Detection of cyanobacteria and their toxin-producing ability using molecular methods has been successfully applied to a diverse range of water and sediment environments. In this study, we use quantitative real time PCR to quantify the abundance of microcystin-producing cyanobacteria and Microcystis, and PCR-denaturing gradient gel electrophoresis technique to investigate the community structure of microcystin-producing cyanobacteria in surface sediment of Lake Taihu in winter. qPCR data showed that Microcystis and microcystin-producing cyanobacteria were present in all of sediment samples and their abundance varied significantly in different lake areas, ranging from 1.23×10⁴copies/g dry weight to 3.75×10⁶copies/g dry weight and from 2.56×10⁴ to 1.07×10⁷ copies/g dry weight, respectively. The proportion of microcystin-producing cyanobacteria to Microcystis ranged from 4.8％ to 35.2％. DGGE patterns indicated that the composition of microcystin-producing cyanobacteria were very similar in surface sediments collected from different lake areas, and the similarity values were between 70.2% and 96.0%. Although the composition of genotypes of microcystin-producing cyanobacteria slightly varied among samples, the dominant band is same. The number of dominant band was negatively correlated with Shannon index. Taking into consideration of qPCR analysis and the concentration of Chlorophyll-a and Phycocyanin, we concluded that in the winter of 2010 cyanobacteria of Lake Taihu mainly overwinter in four lake areas, Mei liang bay, Zhu shan bay,Gong hu bay and center part of Lake Taihu. Our results showed that quantitative real time PCR is a feasible method to investigate the dynamics of toxic cyanobacteria in lake sediment.