The cyanobacterium Microcystis is the most common bloom-forming species in eutrophicated water bodies. Known eco-physiological advantages of this organism help it to compete effectively with other algae and cyanobacteria; however, little is known about the physiological characteristics competence of colonial Microcystis. In the present study, carbonic anhydrase (CA) activity, the affinity for dissolved inorganic carbon (DIC), and the transcription of CA genes were examined in unicellular and colonial Microcystis strains. In comparison with unicellular strains, colonial Microcystis exhibited dramatically higher inorganic carbon affinity at 25 and 35°C, but no significant differences were observed at 15°C. The relative transcription levels of the CA genes icfA1, icfA2, ecaA, and ecaB in all colonial Microcystis were significantly higher than those in unicellular Microcystis at 25 and 35°C. In addition, CA activities of Microcystis increased with temperature, but no significant difference was observed between the unicellular and colonial Microcystis. These results suggest that temperature and phenotypes probably play important roles in the utilization of DIC and trigger the expression of CA genes of Microcystis. The present results may indicate that the capacity for utilizing inorganic carbon plays a role in the persistence or/and succession of different Microcystis blooms.