Field investigations in Lake Taihu (China) were carried out from 1 June 2010 to 15 November 2010 in order to analyze environmental factors related to the succession of Microcystis wesenbergii and M. aeruginosa. M. wesenbergii dominated from the middle of July to the middle of September, and then, M. aeruginosa dominated subsequently. Cell density of M. wesenbergii was high when water temperature was higher than 28 °C, and total dissolved nitrogen:total dissolved phosphorus (TDN:TDP) ratio was below 7 (by weight), but low temperature (lower than 23 °C) was favorable to high cell density of M. aeruginosa. Cell density of M. wesenbergii was low when concentration of total dissolved phosphorus (TDP) was lower than 0.05 mg L−1 and iron concentration was below 0.4 mg L−1; however, cell density of M. aeruginosa was high under these conditions. Our results suggested that temperature and nitrogen:phosphorus (N:P) ratio did not affect the succession of M. wesenbergii and M. aeruginosa. Environmental factors did not explain all of the variation (less than 50 %) and suggested that colonial morphological changes induced by mucilage solubilization should be considered.