Biological capture of CO2 using microalgae is promising approach for mitigation of excess carbon. The aim here was to study the influence of different CO2 (10, 20, and 30% v/v) concentrations as a carbon source on two indigenous isolates of Dunaliella sp. (ABRIINW-CH2 and ABRIINW-SH33) under adjusted pH. Algal growth improved at elevated concentrations of CO2. Resistance response patterns to elevated CO2 concentrations in contents of all the storage products, proline, malondialdehyde (MDA), H2O2, and enzymatic antioxidant activities were different in the studied isolates at different CO2 concentrations. The protein and lipids were high at 10% CO2 concentration, but carbohydrates decreased at 10% CO2 concentration, followed by decrease in protein and lipids and increase in the amount of carbohydrates at 20 and 30% CO2 concentrations. MDA and H2O2 increased significantly at 20 and 30% CO2 concentrations in both isolates, but since MDA in ABRIINW-SH33 isolate was less than that in ABRIINW-CH2 isolate, ABRIINW-SH33 had a higher tolerance to high CO2 concentrations. The increases in catalase (CAT), polyphenol oxidase (PPO), superoxide dismutase (SOD), and proline are the signs of oxidative stress under elevated CO2 concentrations as well as the antioxidative responses in the isolates. In addition, quantitative real-time (qRT)–polymerase chain reaction (PCR) analysis confirmed the biochemical results that elevated CO2 concentration inducted expression of SOD and CAT genes in both isolates under elevated CO2 concentrations. The results clearly showed that two isolates indicated different resistance patterns in response to elevated CO2 concentrations. The molecular and biochemical markers obtained from this study are the basic information that can be used in microalgae strain selection and improvement for CO2 capturing.