The molecular characterization through SSR indicated significant differences among QPM and non QPM for ten lines. The genetic distance and diversity in alleles were detected through microsatellite profiling. The material under investigation possessed considerable amount of variability due to genetic drift acting during random mating of generation, affect the alleles divergence. The presence of ample variability in the test material provided enough scope for selection of genotypes to be used in the future breeding programme for realization of high and stable yields in maize. Based on Jaccard’s coefficient similarity, genetic distances and clustering pattern the genotypes, CM 141 of cluster II is completely distinct from all other inbreeds. Cluster I carried nine inbreeds and consist of two sub clusters. In sub cluster I, there are 3 QPM (KHI 1352, KHI 586, CML395) and 1 non-QPM (V358) inbreeds, as their genetic distance is low. Sub cluster II was constituted by five inbreeds; 2 QPM (CML152, CML140) and 3 non-QPM (V372, V335, V351) showed genetic similarity. Dissimilarity in inbred lines were observed in CM 141 of cluster II, KHI1352 of sub cluster I and CML140 of sub cluster II proved to be promising for use to increased allelic diversity in maize that may be further assessed to develop potential hybrids