The genetic diversity estimates can be useful in important genotypes selection for plant breeders. Eight durum and three bread wheat cultivars were used to study and compare morphological traits with molecular study using SSR technique based genetic diversity estimates. Significant and highly significant differences among wheat genotypes were observed for all traits except flag leaf attitude and outer glume pubescence. Highly significant differences were obtained between durum and bread wheat genotypes for most studied traits. Moderate to low broad-sense heritability estimates were obtained for morphological studied traits. Positive and high significant correlation was found for ear density with foliage color (r= 0.51), waxiness of flag leaf sheath (r= 0.57), waxiness of peduncle (r= 0.60) and peduncle length (r= 0.53), whereas a negative correlation was found between ear density and plant height (r=-0.52, P<0.01). However, waxiness of flag leaf sheath was positively correlated with ear waxiness (r= 0.53, P<0.01), waxiness of peduncle (r= 0.56, P<0.01), and Peduncle length (r= 0.43, P<0.05). The higher polymorphism (90.63%) was found in the B genome than in the A genome (81.97%). Single marker analysis showed that 11 SSR markers were significantly associated with phenotypic traits, including Xgwm111-2B associated with waxiness of peduncle. A significant but low correlation (r = 0.25) was found between the dissimilarity matrix generated from the phenotypic data and that obtained from the SSR markers, suggesting that the characterization based on agromorphological traits and SSR markers will be a useful tool to the breeders for selection of genotypes with appropriate.