The current study was aimed to investigate the DNA polymorphism of C. punctata from three different rivers of northern region of India. For this, C. punctata of river Ganga and its tributaries (river Gomti and river Ken) was carried out using RAPD-PCR (Random amplified polymorphic DNA-polymerase chain reaction). A total of 54 loci were amplified by five selected primers out of 20 having GC content of 60% to 70%. The fish population of river Ganga showed highest genetic polymorphism with 33 (61.11%) polymorphic loci out of 54 loci whereas a total of 55.56% and 46.30% DNA polymorphism were recorded in the fish populations of Ken and Gomti respectively. Maximum genetic identity and minimum genetic distance was recorded between the fish populations of Ganga and Ken showing that these two populations are more similar to each other than to Gomti population. Dendogram based on genetic distance using UPGMA also confirmed that Ganga and Ken population are closer to each other.