The present investigation undertaken at National Research Centre Plant Biotechnology, Pusa, New Delhi in 2005 with the aim of studying inter-relationship existing between the chickpea genotypes. 46 genotypes from chickpea and its wild relatives were collected that include 45 from Cicer arietinum and one from interspecific hybrid (Cicer arietinum x Cicer reticulatum). A total of 11 STMS loci were analyzed, covering various bin locations on different linkage groups. All the 11 STMS loci, in the genetic material under study were found to be highly polymorphic except TA-72. The STMS data was utilized for preparing genetic similarity matrix and further analyzed using UPGMA clustering algorithm. The dendrogram clearly showed 4 large clusters which were divided in sub clusters. Pant G114 and BG 1107 showed remarkable genetic similarity (0.77) followed by II, III and IV. The cluster 1 to 4 comprised of 8, 25,7 and 6 genotypes respectively. The study support greater resolving power of Sequence Tagged Microsatellite Sites molecular markers for chickpea germplasm where very little morphological distinction can be found between the different cultivars.