Spatial and temporal variations of Microcystis species composition in Gonghu Bay and Meiliang Bay in Lake Taihu were observed from July 2010 to June 2011. The relationship between seasonal succession of Microcystis colonies and environmental factors was also analyzed. The results showed that M. ichthyoblabe, M. wesenbergii and M. aeruginosa were dominated successively during July to September, and only M. ichthyoblabe and other Microcystis can be found in winter and early spring. CCA analysis revealed that temperature was the main factor driving this seasonal succession. No difference was found in spatial distribution of Microcystis between the two bays, nor was that between the central and coastal areas in the same bay. However, the cell abundance of Microcystis in the downwind area was greater than that in the upwind area, especially that of M. wesenbergii and M. aeruginosa. The size of M. wesenbergii and M. aeruginosa colonies was relatively larger, which made them float to the surface and migrate by the wind much easier. Thus, it was concluded that surface migration caused by wind was an important factor in the spatial distribution of Microcystis colonies.