Cell density, morphospecies and colony size of Microcystis at different depths in Lake Taihu were investigated from spring to winter 2011 to identify differences in Microcystis morphospecies compositions at different depths and their causes. Microcystis ichthyoblabe, Microcystis wesenbergii and Microcystis aeruginosa successively dominated the water surface from June to October. However, the percentage of both M. wesenbergii and M. aeruginosa did not exceed 50 % in the mesosphere when M. wesenbergii and M. aeruginosa dominated the surface successively. M. ichthyoblabe dominated the water bottom from late spring to late autumn, while other Microcystis (including other Microcystis morphospecies and some small colonies that could not be identified) dominated the water bottom at other times. The colony size of other Microcystis showed little change during the study period and D50 (the colony size at which 50 % of the total mass of the particles was smaller than this size) was always smaller than 100 μm. D50 of M. ichthyoblabe was about 200 μm at most times, but reached 400 μm in early November. Colony size of M. wesenbergii and M. aeruginosa increased and then decreased, with the maximum D50 of 700 μm and 800 μm, respectively, occurring in October. Vertical distribution of cell density and colony sizes of different Microcystis morphospecies were also comparatively analyzed, and the results suggested that the Microcystis morphospecies composition varied with depth, with large Microcystis morphospecies dominating the water surface because of their large colony size.