The common carp (Cyprinus carpio L.) is one of the major aquaculture species, contributing nearly 35% to the inland fish production in Karnataka, India. Stocks collected from Hungary (2), Indonesia and Vietnam were assessed alongside two local stocks in a series of culture performance trials with the objective of setting up a base population for developing a breeding programme. The present study deals with the genetic divergence and polymorphism in these six stocks using random-amplified polymorphic DNA (RAPD) markers. A total of 180 decamer random primers were screened for polymerase chain reaction (PCR) amplification (OPA 1-20, OPB1-20, OPC1-20, OPD1-20, OPE1-20, OPF1-20, OPG1-20, OPP1-20 and OPM1-20). Eight primers were selected for analysis of common carp genotypes (OPA-7, OPA-20, OPB-17, OPF-10, OP F-9, OPG-4, OPG-9 and OPP-16). Out of 492 bands recorded, 57.1% were polymorphic. Stepwise regression analysis was carried out to find best combination markers affecting body weight (P < 0.001). The results demonstrate major differences in the genetic structures between different stocks. Dendrogram data showed grouping of individuals according to stocks and corresponding data variables revealed the per cent homology within the stock and also found markers correlating to the body weigh

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