In order to monitor the changes of Microcystis along with temporal and spatial variations, seasonal variation of Microcystis in Lake Taihu was investigated by 16S-23S rRNA intal transcribed spacer denaturing gradient gel electrophoresis (16S-23S rRNA-ITS DGGE) and microscopic evaluation. Samples were collected quarterly at four sites (River Mouth, Meiliang Bay, Cross Area, and Lake Center) from August 2006 to April 2007. Results showed that Microcystis dominated total phytoplankton abundance at the four sites in all seasons except winter. The average annual abundance of Microcystis was relatively high at River Mouth and Meiliang Bay, reaching 81.22×106 and 61.32×106 cells/L, respectively. For temporal variations, Shannon-Wiener diversity index (H’) according to DGGE profile revealed the richness of Microcystis in summer (H’=1.375±0.034) and winter (H’=1.650±0.032) was lower than that in spring (H’=2.078±0.031) and autumn (H’=2.365±0.032) (P<0.05). While for spatial variations, the richness of Microcystis at River Mouth (H’=2.015±0.074) was higher than at other sites during four seasons (P<0.01). Very few differences of Microcystis diversity in the same season were observed among the other three sites (P>0.05). Canonical correspondence analysis (CCA) was performed to elucidate the relationships between Microcystis operational taxonomic units (OTUs) composition and the environmental factors. Results of CCA revealed that temperature was strongly positively correlated with the first axis (r=0.963), while TSS was negative correlated with the second axis (r=-0.716). Phylogenetic tree based on the sequencing results of target bands on DGGE gel indicated that samples collected in summer and winter constituted two separated clusters.