Rising atmospheric CO 2 concentrations are likely to affect many ecosystems worldwide. However, to what extent elevated CO 2 will induce evolutionary changes in photosynthetic organisms is still a major open question. Here, we show rapid microevolutionary adaptation of a harmful cyanobacterium to changes in inorganic carbon (C i ) availability. We studied the cyanobacterium Microcystis, a notorious genus that can develop toxic cyanobacterial blooms in many eutrophic lakes and reservoirs worldwide. Microcystis displays genetic variation in the C i uptake systems BicA and SbtA, where BicA has a low affinity for bicarbonate but high flux rate, and SbtA has a high affinity but low flux rate. Our laboratory competition experiments show that bicA + sbtA genotypes were favored by natural selection at low CO 2 levels, but were partially replaced by the bicA genotype at elevated CO 2 . Similarly, in a eutrophic lake, bicA + sbtA strains were dominant when C i concentrations were depleted during a dense cyanobacterial bloom, but were replaced by strains with only the high-flux bicA gene when C i concentrations increased later in the season. Hence, our results provide both laboratory and field evidence that increasing carbon concentrations induce rapid adaptive changes in the genotype composition of harmful cyanobacterial blooms.climate change | harmful algal blooms | Microcystis aeruginosa | microevolution | natural selection