The highly efficient CO₂ concentration mechanism (CCM) gives cyanobacteria a competitive advantage under low CO₂ conditions. However, with the rapid increase in atmospheric CO₂ concentration, little information has been presented on how the CO₂ concentration mechanism of cyanobacteria responds. Therefore, this study takes a common blooming cyanobacterium, Microcystis, to investigate in the present by monitoring the dynamic changes and different CCM genotypes of Microcystis in Lake Dianchi. At the same time, the microevolutionary characteristics and dynamic changes of CCM genotypes in Microcystis were also discussed. Furthermore, the competing effects of different CCM genotypes in Microcystis at high (0.08%), medium (0.04%) and low (0.02%) CO₂ concentrations (V/V) were compared. The results showed that the concentration of inorganic carbon (IC) in Lake Dianchi was spatially variable at four sampling sites, but all sites showed a trend of first decreasing and then increasing IC concentrations, and HCO^-₃ was the major form of IC. At the four sampling sites of DDH, GYS, LLH and STS, the sbtA genotype Microcystis was dominant and its relative abundance was much higher than that of the bicA genotype Microcystis. In different bloom periods, the bicA and sbtA genotypes of Microcystis showed opposite trends, i.e. the relative abundance of the sbtA genotype Microcystis gradually increased from early to mid- bloom, while the bicA genotype Microcystis increased only in late bloom. The competition experiments showed that the bicA genotype had an apparent competitive advantage in a high CO₂ environment and showed a trend of transition from the bicA genotype to the sbtA genotype with decreasing CO₂ concentration. These indicate that the IC concentration was relatively low in the middle of the bloom period, resulting in the sbtA genotype showing a competitive advantage in a carbon-limited environment, while the bicA genotype, a sensitive type to changing CO₂ concentration, gradually increased with increasing IC concentration. In addition, the genotypes of Microcystis showed a bicA→sbtA→bicA transition during different Microcystis bloom periods in Lake Dianchi due to the effects of total alkalinity, pH and Chl.a. These results suggest that Microcystis can maintain its competitive advantage and sustain the bloom by regulating the algal strains with different CCM genotypes in response to the IC concentration in the water.