Comet and Micronucleus assays have been used to assess DNA damage in Catla catla and Cirrhinus mrigala collected from polluted areas. Heavy metals Cd, Cu, Mn. Zn, Pb, Cr, Sn and Hg were detected by atomic absorption spectrophotometry in River Chenab water. All physicochemical parameters and heavy metals were found beyond the tolerable limits. Comet assay showed significant (p<0.05) DNA damage in Catla catla as 17.33±2.42, 11.53±2.14 and 14.17% DNA in tail. Tail moment was 10.06±2.71, 3.11±0.74 and 14.70±1.89, Olive moment was 8.85±1.84, 3.83±0.76 and 7.11±0.73, respectively. Highly significant (p<0.01) damage was reported in Cirrhinus mrigala as 37.29±2.51%, 34.96±2.53% and 38.80±2.42% DNA in comet tail, tail moment was 23.48±3.90, 19.78±4.26 and 14.30±1.82, olive moment as 16.22±2.04, 13.83±1.96 10.99±0.90 from three different sites of the polluted area of the River Chenab. Significant (p<0.05) differences were reported polluted and farmed fish but non-significant (p>0.05) differences in farmed and non-polluted upstream. Micronucleus assay showed similar findings for single and double micronucleus induction as 23.20±4.19, 2.80±1.07 in Catla catla and 44.80±3.73, 06.20±0.97/thousand cells, respectively in Cirrhinus mrigala. Nuclear abnormalities were found as 6.00±0.84 and 09.60±1.72/thousand cells, respectively in both species. These findings infer that these novel fish DNA damage assays to detect genotoxicity, could be used as expedient toxicity screening of aquatic environments.