Five microsatellite loci (MFW1, MFW3, MFW4, MFW5 and MFW7) were used to study the genetic diversity and characterization of different strains (Maharashtra, Local, Koi and Amour) of common carp (Cyprinus carpio L.). The average number of alleles across all loci was highest in Koi (11.4) followed by Maharashtra (11.0) and Local strains (9.0). The amour had lowest (6.2) mean number of alleles. The mean observed heterozygosity (Ho) ranged between 0.45 and 0.62, while expected heterozygosity (He) 0.32-0.68. Polymorphic information content mean values varied from 0.58 to 0.74. The Nm and the FST values indicated a low level of gene flow and high level of differentiation. The highest genetic distance was observed between the Amour and the Local strains, while the lowest was between Maharashtra and Local strains. The FST value ranged between 0.028 and 0.207.The common carp, Cyprinus carpio is a freshwater Cyprinid originated from Eurasia. This is an exotic spp. in Indian waters and its gene pool is expected to change due to isolation and adaptation process. To monitor the genetic changes, different types of genetic markers especially microsatellite are used. In the past decade, microsatellites have become a preferred tool for breeding applications and genetic fingerprinting due to their high information content. Microsatellite markers allow for fingerprinting animals for traits reflecting genotypic differences irrespective of phenotype displayed and provide a molecular means of tracking heritable elements. This guidance is important in the selection of brood stock since it improves the accuracy and quality of the breeding prediction for future generations. The aim of the study was to obtain insight into the relationships within and among different strains of common carp. The strains of common carp (Maharashtra, Local, Koi and Amour) maintained at Aquaculture Research and Seed Unit, Directorate of Research, MPUAT, Udaipur were used for present study. The caudal fin (approximately 100 mg) samples from 80 (20 from each strain) common carp were collected. The fin samples were kept in Eppendorf micro-tubes with absolute ethanol. Genomic DNA was extracted from tissue using a protinase K, phenol: chloroform protocol [1].Polymerase chain reaction (PCR) was done in a C1000 TM Real Time PCR (Bio-Rad) and reactions carried out in 15 ll reaction volume containing 10.88 ll of mili Q water, 1.5 ll of 1 9 PCR buffer, 0.6 ll of dNTP, 0.4 ll of reverse primer (0.3 pmol), 0.4 ll of forward (M-13 labeled) primer (0.3 pmol), 0.2 ll of tailed primer (0.3 pmol) 0.2 ll Taq and 1.0 ll of template. The amplification conditions recommended by Crooijmans et al. [2] were followed with some modification especially in annealing temperature. The PCR cycles were: pre-amplification denaturation at 94°C for 3 min, then 30 s at 94°C, 30 s at the respective annealing temperature (56°C