Pigeon pea (Cajanus cajan L.) is major pulse crops of the tropics, and is important in small-scale farming in mainly developing, semi-arid regions. The RAPD analysis of genomic DNA by 3 RAPD primers showed good polymorphism in 5 pigeon pea cultivars namely as Vipula, ICPL-87, BSMR-853, BSMR-736, Rajeshwari. Total 14 amplicons were generated by 3 primers (OPC-11, OPC-9 and OPC-1). Out of them 12 amplicon were found to be polymorphic showing 85.71% polymorphism, the Jaccard similarity coefficient among all genotypes ranged from 0.35 to 0.77. The highest genetic similarity to an extent of 77% was recorded between Vipula and ICPL-87 isolates followed by 64% similarity between BSMR-736 and BSMR-853. The dendrogram based on Jaccard similarity coefficient produced 2 main clusters A & B. Cluster A divided into two sub clusters A1 and A2. The sub cluster A1 shows two genotype Vipula, ICPL-87 and sub cluster A2 to contains only BSMR-853. The cluster B comprised of two genotype BSMR-736 and Rajeshwari showing the similarity about 51%.