Lake Taihu, which is the third largest freshwater lake in China, has experienced extensive cyanobacterial (Microcystis spp.) blooms over the past two decades. However, the distribution, dynamics and succession of the blooms have not been fully studied. To better understand the basic characteristics of Microcystis blooms in Lake Taihu, samples were collected from December 2008 to December 2009. The distribution and dynamics of different Microcystis morphotypes were characterized. Microcystis genotypes were analyzed also by sequencing the clone library of the internal transcribed spacer of the rRNA operon (ITS). The abundance of total Microcystis and the proportion of microcystin-producing subpopulation were estimated by using a quantitative PCR assay. Marked succession in both morphotypes and genotypes of the Microcystis population occurred during the course of the Microcystis bloom. The 2337 ITS sequences were obtained and were revealed to contain 618 Microcystis genotypes, which was the highest Microcystis genetic diversity reported in Lake Taihu. The T1 genotype, which was characterized by strains of Microcystis floc-aquae, was the most dominant genotype during winter and spring around the entire lake and likely acted as the main inoculum for forming blooms the following year. Water temperature periodically affected the succession of both Microcystis genotypes and morphotypes, whereas the micro environment influenced the spatial distribution of Microcystis genotypes and morphotypes. High ratios of mcyD containing Microcystis subpopulations were detected during the onset and later bloom phases. A redundancy analysis (RDA) indicated that the water temperature and PO4-P were the major factors controlling both the total Microcystis abundance and the proportion of microcystin-producing Microcystis in hyper-eutrophic waters. (C) 2016 Elsevier Ltd. All rights reserved.