Although biomass variations in Microcystis and microcystin have been widely reported, few studies have addressed whether different trophic states of natural lake water affect the spatial-temporal variations in abundances of microcystin-producing Microcystis in a given bloom. In this study, we used a harmful algal bloom in Chaohu Lake, eastern China, as an example to investigate the mutual relationship between different nutrient states and environmental factors, and the impact on Microcystis. Overall, cyanobacteria and Microcystis were more abundant in the middle and western parts of the lake under high nutrients levels, while in the eastern part, nutrient concentrations were low enough to limit biomass, and their fluctuations affected the contents of toxic Microcystis. Moreover, microcystin concentration was correlated positively to nutrient levels and Microcystis biomass during bloom developing in 2013 from June to August. Temporally, the cellular content of total microcystin was lowest when the bloom peaked in intensity. Our results suggest that lake eutrophication not only results in cyanobacterial blooms, but may also increase the proportion of toxic Microcystis species and their cell-bound MCs contents (i. e. microcystin cell quotas) under mild eutrophication. The present investigation provided molecular evidence for the selection of MC-producing and non-MC-producing genotypes. The current study provides new evidence advocating the monitoring of partitions of large lakes when studying cyanobacteria and toxin-contaminated freshwaters, which will be benefi cial for both water agencies and water researchers.