Inactivation of the sigC gene (sll0184), encoding the group 2 sigma factor SigC, leads to a heat-sensitive phenotype of Synechocystis sp. PCC 6803. Cells of the ΔsigC strain grew poorly at 43 °C at pH 7.5 under ambient CO2 conditions. Addition of inorganic carbon in the form of 3 % CO2 or use of an alkaline growth medium (pH 8.3) restored the growth of the ΔsigC strain at 43 °C. These treatments compensate for the low concentration of inorganic carbon at high temperature. However, addition of organic carbon as glucose, pyruvate, succinate or 2-oxoglutarate did not restore growth of the ΔsigC strain at 43 °C. In the control strain, the amount of the SigC factor diminished after prolonged incubation at 43 °C if the pH of the growth medium was 7.5 or 6.7. Under alkaline conditions, the amount of the SigC factor remained constant at 43 °C and cells of the control strain grew better than at pH 7.5 or pH 6.7. The pH dependence of high-temperature growth was associated with changes in photosynthetic activity, indicating that the SigC factor is involved in adjustment of photosynthesis according to the amount of available inorganic carbon. Our results indicate that acclimation to low inorganic carbon is a part of acclimation to prolonged high temperature and that the SigC factor has a central role in this acclimation.