The ability of populations to persist and adapt to environmental changes is based on genetic diversity. Substantial empirical data shows that the genetic integrity of natural fish population is being compromised by the effect of anthropogenic interventions and robust environmental conditions. Genetic diversity estimates were obtained for 210 individuals of Cyprinus carpio sampled from six sites of Indus river basin, using 14 microsatellite loci as markers. The results showed a moderate level of genetic diversity in terms of number of alleles (Na), effective number of alleles (Nae) and heterozygosity (H). Significant deviation from Hardy Weinberg equilibrium was observed in 17 out of 84 tests. The pairwise FST values showed a moderate level of population differentiation. AMOVA revealed a significant genetic structuring among the wild populations. The UPGMA dendrogram constructed for analysis of genetic relatedness grouped all the populations into two clusters. The understanding of genetic structure of C. carpio in natural systems would be instrumental in genetic enhancement programs, effective management and sustainable conservation of riverine genetic resources.