Twenty eight lines including 8 A lines, 8 B-lines and 12 R-lines newly developed at station were characterized by with 21 SSR primers. A total number of alleles detected by the aforesaid primers were 63 with maximum and minimum frequency of 5 and 2, respectively. The maximum and minimum PIC Values were found to be 0.994 and 0.138 for the primers CCB-3 and CCB-5 respectively. Average genetic similarity coefficient from all possible combinations was found to be 0.563. Among the 21 primers, 9 were found polymorphic for 28 genotypes. Genetic similarity coefficient for most of number of pairs was in the range of 0.86 to 1.00, indicating diversity among the chosen genotypes. All the 28 genetic lines could be easily distinguished from each other based on the selected markers and thus were effective for varietal identification and diversity analysis of pigeonpea genotypes. A dendogram based on loci profile showed good agreement with their cultivars pedigree information.

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