Biodiversity among 32 sesame (Sesamum indicum L.) genotypes; 30 accessions were obtained from various regions of Egypt and two local cultivars were assessed agronomically using different morphometric and yield-related traits. Significant variations were observed for all these traits such as plant height, plant weight, No. of pods, pod weight and oil percentage. The variation between highest and lowest genotype in plant height was almost 50%, as genotype V32 recorded the highest plant height (220 cm), whereas genotype V19 was the shortest one (100 cm). Plant weight ranged from 802.2 to 99.5 g in V6 and V16, respectively. Pod weight varied from 202.6 to 32.2 g in V4 and V15, respectively. No. of pods ranged from 75.7 to 10.3 in V5 and V17, respectively, while oil percent varied from 60% to 40.5% in V11 and V3, respectively. Using morphometric characteristics, the genotypes were grouped into two main clusters with high variation among them. Fifteen out of the 32 genotypes were chosen and subjected to ISSR and SRAP analyses to detect the level of genetic diversity in relation to geographical origins using 11 ISSR and 7 SRAP primers. ISSR primers generated 46 amplified bands. Four out of these primers were resulted in 5 unique markers among the 15 sesame genotypes. Molecular characterization revealed a polymorphism percentage of 46.66% for ISSR markers, while SRAP primers exhibited a total of 22 bands and one out of these primers revealed 3 unique genotype specific marker polymorphism was calculated as 50%. The cluster analysis showed a high genetic diversity among the sesame genotypes and their diversity was consistent with their source pedigrees. The results of principal component analysis (PCA) were closely aligned with those of the cluster analysis. Considering the relatedness of genotypes, geographical origin and their morphological characteristics reflected to the similarity of ISSR and SRAP patterns.