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The genetic interrelationship among all the popular vegetable cowpea varieties cultivated in Kerala was investigated through morphometric, RAPD and SSR analyses. High polymorphism was observed in RAPD (88.0 per cent of bands were polymorphic) and SSR (80.0 per cent of bands were polymorphic) analyses. Dendrogram based on morphological parameters has divided the genotypes into two main clusters which truncated at 68.0 per cent similarity, with purple and green poded varieties segregating into separate clusters. Morphometric analysis was successful to group the varieties with determinate and indeterminate growth habits whereas, RAPD and SSR markers could not make a clear division. However, distinction was apparent between purple poded and green poded types and purple poded varieties viz Vyjayanthi and Varun exhibited high similarity with each other in SSR analysis (80.0 per cent) when compared to RAPD (77.0 per cent). Dendrogram of pooled data of SSR and RAPD analyses has revealed maximum similarity between Vyjayanthi and Varun (77.0 per cent).