The assessment of genetic diversity is a primary concern of plant breeders and germplasm curators for which morphological traits are internationally accepted descriptors but are often associated with limitations due to G ${ imes}$ E interactions. Phenotypic, ISSR, and SSR markers were employed to determine the genetic diversity and relationships among 20 commercially cultivated sesame genotypes representing different geographical regions of India. A narrow range of genetic dissimilarity (0.01 - 0.12) with mixed clustering was observed using morphological descriptors. A total 279 band positions with 57% polymorphism was amplified by ISSR primers, whereas 36 allelic positions with 73% polymorphism were produced by SSR primers with 100% reproducibility. The ISSR primers with high discrimination power were identified producing genotype-specific bands and distinguishing all the sesame genotypes used in this study. A poor correlation and lack of perfect congruence between phenotypes and marker-based analysis was indicated by the UPGMA dendrogram and PCA analysis. Our results suggest that SSR and ISSR markers provide a powerful tool for genotype identification and establishment of genetic relationships among sesame genotypes. We recommend the use of molecular markers for testing, required for obtaining intellectual property rights, and also for the analysis of genotypic diversity among sesame varieties.