Malathion [S-(1,2-dicarboethoxyethyl) O, O-dimethyl phosphorodithioate] is a widely used organophosphorus insecticide throughout the world. However, limited efforts have made to study its genotoxic effect in different fish tissues. The present investigation was aimed to assess the genotoxic potential of the pesticide to the freshwater teleost fish Channa punctatus at sublethal concentrations using the micronucleus test and comet assay. Initially, the 96-h LC50 value of commercial-grade malathion (50% EC) was determined as 5.93 ppm in a semistatic system. Based on LC50, three test concentrations (viz. sublethal I, sublethal II, and sublethal III) were determined to be 1.48, 0.74, and 0.59 ppm, respectively, and the fish specimens were exposed to these concentrations. Tissue samplings were done on days 0, 1, 3, 7, 15, 22 and 29 of malathion exposure for assessment of the induction of micronuclei (MN) frequency and DNA damage. The MN formation in the peripheral blood cells was found to be significantly higher (p < 0.05) in the treated specimens at all sampling intervals compared to the control. The MN frequency reached maximum on days 3 and 7 at sublethal I and II concentrations, respectively, followed by a nonlinear decline with the progression of the experiment. Similarly, significant effects (p < 0.05) of both concentration and time of exposure were observed on DNA damage in the gill, kidney, and lymphocytes. All of the tissues exhibited a concentration-dependent increase in DNA damage up to day 3, followed by a nonlinear decrease with the duration of exposure. A comparison of the extent of DNA damage among the tissues showed the sensitivity of gill tissue to malathion.