At the beginning of this century, the atmospheric CO₂ concentration had increased by 40% compared with that in the pre-industrial era, and at the end of this century it is expected to reach 550-900 μmol/mol. The temperature is also expected to increase by 1.6-7.0℃. To date, much research has focused on the effects of elevated CO₂ or/and elevated temperature on the growth, physiology, and ecology of cyanobacteria, but little is known about the combined effects of these factors on the ability of cyanobacteria to repair damage caused by ultraviolet (UV) radiation. In this study, Synechocystis sp. PCC6803 was grown for 15 weeks under five different conditions: (1) 25℃+ 400 μmol/mol CO₂ (control group); (2) 29℃+ 400 μmol/mol CO₂; (3) 25℃+800 μmol/mol CO₂; (4) 29℃+ 800 μmol/mol CO₂; and (5) 25℃ +1200 μmol/mol CO₂. Total RNA was extracted from cyanobacteria in each treatment, and was used to synthesize cDNA. Then, the transcript levels of four UV damage repair genes (phrA/psbA1/psbA2/psbA3) and the 16S rRNA gene were determined by Taqman absolute quantitative polymerase chain reaction. The results indicated that the transcript levels of 16S rRNA were 60%-85% lower in all the tested groups than in the control group. Except for the phrA gene in the 29℃+ 400 μmol/mol CO₂ treatment, all four UV damage repair genes showed transcript levels approximately 50% lower in all the treatments than in the control group. Our key findings were as follows: 1) Among the four UV damage repair genes, psbA2 showed the largest decrease in transcript levels in the treatments, followed by the psbA3 gene; 2) the combined effects of increased temperature and elevated CO₂ counteracted the effects of each individual factor on the transcript levels of the psbA3/psbA2 gene and the 16S rRNA gene. For instance, at 29℃, the transcript level of psbA3 was about 82% lower than that in the control group; at the CO₂ concentration of 800 μmol/mol, the transcript level of psbA3 was approximately 93% lower than that in the control group; however, the transcript level of psbA3 was only 73% lower than that in the control group in the 29℃+ 800 μmol/mol CO₂ treatment. 3)When the CO₂ concentration increased from 800 to 1200 μmol/mol, there were marked decreases in the transcript levels of the four UV damage repair genes and the 16S rRNA gene. 4) Unlike psbA2/psbA3, the transcription of the psbA1 gene is thought to be unaffected by environmental factors, except for microaerobic conditions. However, we found that the transcript level of psbA1 was 50% lower in the29℃ + 800 μmol/mol CO₂ treatment than in the control group. Taken together, our results indicate that the greenhouse effect will likely decrease the ability of cyanobacteria to repair UV damage and synthesize ribosomes. The effects of elevated CO₂ concentrations may be somewhat counteracted by increased temperatures. This is a topic worthy of further research. The transcript levels of the 16S rRNA gene significantly decreased under the elevated CO₂ concentrations and increased temperature in these experiments. Therefore, further experiments should be conducted to test its reliability before using it as an internal reference gene in studies on the effects of global change on gene expression in cyanobacteria.