The role of the primary-like sigma factor SigC was studied in Synechocystis. Under high temperature stress (48 °C) the ΔsigC inactivation strain showed a lower survival rate than the control strain. The ΔsigC strain grew poorly at 43 °C in liquid cultures under normal air. However, change to 3% CO2 enhanced growth of ΔsigC at 43 °C. Differences in expression of many genes related to the carbon concentrating mechanisms between the control and the ΔsigC strain were recorded with a genome-wide DNA microarray. We suggest that low solubility of CO2 at high temperature is one of the factors contributing to the poor thermotolerance of the ΔsigC strain.