The present study investigated the intertissue differences in genotoxicity induction in the fish, Channa punctatus, in response to 4-nonylphenol. The lethal concentration of 50 (LC) was estimated using a semi-static system. Fish were subjected to three sublethal concentrations of 4-nonylphenol (NP) for 24, 48, 72, and 96 h. Liver, gill, and kidney tissues were analyzed, and the genotoxicity was estimated using the micronucleus test and the comet assay. The frequency of micronucleated cells (MNCs), binucleated cells (BNCs), aberrant cells, and tail moment (TM) increased significantly. The time for maximum induction of genotoxicity for all the parameters considered in the micronucleus assay was 72 h of exposure, whereas the TM was highest at 24 h of exposure followed by a decline. The gill and liver showed higher genotoxicity than kidney tissue demonstrating organ-specific susceptibilities to NP in fish C. punctatus.