Abstract: The continuous rise of atmospheric CO₂ concentration will alter the physiological and ecological response in cyanobacteria. The CO₂ concentration mechanism (CCM) of cyanobacteria is one of the important competitive advantages in the formation of water bloom. Different transport systems in the CCM of cyanobacteria have different characteristics. For example, bicA is a bicarbonate transporter with high throughput and low affinity, while sbtA with high affinity but low throughput. In order to explore the relationship between different inorganic carbon (Ci) transport genotypes of cyanobacteria and pH changes in lake water, this paper optimized the detection protocol of the relative abundance of cyanobacteria with different inorganic carbon transport genotypes in water. We measured the relative abundance of various cyanobacteria species with different Ci transport genotypes in Taihu Lake, Dianchi Lake and 18 lakes in Wuhan, and combined with the pH value in the water body to analyze the response of different Microcystis genotypes to CO₂ changes. It was showed that bicA strains, sbtA strains and bicA+sbtA strains all exist simultaneously in the sampled lakes, and the sbtA strains was the most widely distributed. With the increase of pH in water, the dominance of sbtA strains increased. In order to further analyze the response of different Ci transport genotypes of cyanobacteria to the change of CO₂ concentration, we studied the competition of bicA strains, sbtA strains and bicA+sbtA strains under high concentration (1000 ppm) and low concentration (100 ppm) carbon dioxide respectively. The results showed that sbtA strains had obvious competitive advantage at low Ci level, while bicA strains occupied a dominant position at high Ci level. Our study showed that with the increase of CO₂ concentration, bicA strains in cyanobacteria bloom would have a competitive advantage. Therefore, we predict that the increase of atmospheric CO₂ concentration will affect the community composition of bloom cyanobacteria.