Simple sequence repeats (SSRs) are valuable genetic markers due to their co-dominant inheritance, multi-allelic and reproducible nature. They have been largely used for exploiting genetic architecture of plant germplasms, phylogenetic analysis, and mapping studies. Among the SSRs, di-nucleotide repeats are the most frequent of the simple repeats distributed throughout the plant genomes. In present study, we aimed to discover and develop di-nucleotide SSR markers by using the whole genome re-sequencing (WGRS) data fromCicer arietinumL. andC. reticulatumLadiz. A total of 35,329 InDels were obtained inC. arietinum,whereas 44,331 InDels inC. reticulatum. 3387 InDels with 2 bp length were detected inC. arietinum, there were 4704 inC. reticulatum. Among 8091 InDels, 58 di-nucleotide regions that were polymorphic between two species were selected and used for validation. We tested primers for evaluation of genetic diversity in 30 chickpea genotypes includingC. arietinum,C. reticulatum, C. echinospermumP.H. Davis,C. anatolicumAlef.,C. canarienseA. Santos & G.P. Lewis,C. microphyllumBenth.,C. multijugumMaesen,C. oxyodonBoiss. & Hohen. andC. songaricumSteph ex DC. A total of 244 alleles were obtained for 58 SSR markers giving an average of 2.36 alleles per locus. The observed heterozygosity was 0.08 while the expected heterozygosity was 0.345. Polymorphism information content was found to be 0.73 across all loci. Phylogenetic tree and principal coordinate analysis clearly divided the accessions into four groups. The SSR markers were also evaluated in 30 genotypes of a RIL population obtained from an interspecific cross betweenC. arietinumandC. reticulatum.Chi-square (χ2) test revealed an expected 1:1 segregation ratio in the population. These results demonstrated the success of SSR identification and marker development for chickpea with the use of WGRS data. The newly developed 58 SSR markers are expected to be useful for chickpea breeders.