Microcystins (MC), the most prevalent group of harmful cyanobacterial hepatotoxins, are primarilyproduced by strains of cyanobacteria in Microcystis, Anabaena and Planktothrix. Lake Taihu, which is thethird largest freshwater lake in China, is a hypertrophic shallow lake in eastern China that hasexperienced lake-wide cyanobacterial blooms annually during the last few decades. In this study, PCRDGGEwas used to evaluate the diversity of potential MC-producing cyanobacteria and real-time PCRwas used to analyze the dynamics of this population based on the presence of the mcy gene in samplescollected during a year long study. The results revealed that all MC-producing genotypes detectedbelonged to the genus Microcystis. In addition, the MC-producing genotype communities were morediverse during the bloom season than the non-bloom season, and the diversity in the late bloom periodwas lower than the diversity in the early bloom period. Furthermore, the abundance of MC-producinggenotypes increased dramatically during the bloom development period, reaching its peak in latesummer (September). The results also suggested that the highest mcy gene concentration lagged behindthe highest MC concentration, and the potential MC-producing cyanobacterial community shift laggedbehind the development of blooms.