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The cyanobacterium Microcystis, which occurs as colonies of different sizes under natural conditions, can produce toxic microcystins (MCs). To monitor the toxicity and assess the risk of Microcystis blooms in Lake Taihu, it is important to investigate the relationship between MC production and Microcystis colony size. In this study, we classified Microcystis collected from Zhushan Bay of Lake Taihu during blooms into four classes with size of <50 μm, 50–100 μm, 100–270 μm and >270 μm and studied their differences in MC production and genetic structure. The results showed that colonies with size of <50, 50–100, 100–270 and >270 μm produced 12.2 ± 11.2%, 19.5 ± 7.9%, 61.3 ± 12.6%, and 7.0 ± 9.6% of total MC, respectively. The proportion of cell density of colonies with size of 50–100, 100–270 and >270 μm was positively correlated with MC concentration during blooms, while that of colonies with size of <50 …