The pH of chlorination is an important factor affecting the formation of disinfection byproducts (DBPs). In this study, we discovered that the genotoxicity induced by chlorination can be effectively reduced under alkaline conditions. As the pH of chlorination increased from 6.5 to 8.5, the genotoxicity of investigated waters reduced by ∼30–90 %. By assessing the genotoxicity of the mixture of measured DBPs, it was found that the contribution of measured DBPs to the overall genotoxicity was lower than 5 %, and the significant reduction of genotoxicity was largely associated with unknown DBPs. The result of Pearson's correlation analysis indicated that humified organics and soluble microbial byproducts were likely responsible for the genotoxicity, and their derived genotoxic compounds (i.e., unknown DBPs) tended to decompose during alkaline chlorination. However, the control of genotoxicity by alkaline chlorination was achieved at the expense of promoting trihalomethane (THM) formation. The highest genotoxicity reduction (93 %) was observed for chlorinated granular activated carbon-treated waters, but the formation of THMs was promoted to a level approaching that in untreated waters. The inconsistent trend of overall genotoxicity and THM concentration during alkaline chlorination suggested the inadequacy of THMs as metric for DBP exposure, and considerations should also be given to the toxicity of bulk water in addition to regulated DBPs.