Possible methods to minimize the toxic effects of SOx and NOx on the growth of a highly CO2 tolerant and fast-growing microalga, Chlorella sp. KR-1, were investigated. Maintaining the pH of the culturing media at an adequate value was quite important to enhancing the tolerances of the microalgae to SOx and NOx. Controlling the pH by adding an alkaline solution, using a low flow rate of gas fed to the culture, and using a high concentration of inoculating cells were effective methods to maintaining the proper pH of the culture. Controlling the pH was the most effective method but could be applied only for some specific microalgae.