Phenotypic and genetic diversity of thirty diverse short duration chickpea cultivars and breeding lines were assessed using twelve agro-morphological characters and STMS primers. Phenotypic diversity was assessed by Mahalanobis’s D2-statistics in two contrasting environments (E1 and E2) using grain yield and other agronomic characters. Mahalanobis’s D2 analysis revealed that 30 genotypes were grouped into eight clusters at E1 and 5 clusters at E2. The distance values for all the 435 pairs of genotypes for different traits at E1 ranged from 2.0 between ICCV2 and BGD9920 to 19.1 between ICCV4958 and Karikadale and at E2 it ranged from 0.7 between BGD9706 and JG11 to 47.9 between BGD132 and BG1103. Crossing between these genetically diverse genotypes may result in promising derivatives for grain yield and other agronomically important traits. The genetic diversity studies using STMS markers revealed that among the primers used PIC was highest for the STMS primer CAM0443 and CAM0886, which indicated that these primers might be an effective and useful tool to determine the genetic differences among the genotypes and to study the phylogenetic relationship. The STMS marker profiles resulted in seven clusters at nearly 52 per cent similarity revealing that the presence of genetic diversity at molecular level was high among the selected genotypes. The highest similarity index was observed between BGD72 and Annigeri-1 whereas the lowest similarity index between BGD9920 and ICC92944. The correlation between morphological and STMS dissimilarity matrices was positive 0.079 and non-significant (p< 0.001, random permutations) for both locations suggesting that the two systems gave different estimates of genetic relations among the genotypes.