Plant genetic diversity of crops and their wild relatives are important sources of variability for breeding purposes. However, the amount and structure of genetic diversity in most crops is still to be determined. The goal of this work was to study genetic diversity of cultivated barley, and in its ancestor, wild barley. Specifically, we estimated genetic diversity within and among populations at molecular markers and at quantitative traits. We used 353 advanced inbred lines of barley from 19 breeding programs around the world, and 280 genotypes of wild barley from 23 natural populations of the Middle East. A total of 80 SSR markers and 21 quantitative traits were evaluated in all genotypes. For each species, the level of polymorphism, genetic diversity, and among population differentiation was computed. Polymorphism and genetic diversity for barley was 0.80 and 0.32 respectively, while for wild barley it was 0.79 and 0.37 respectively. Among population diversity corresponding to Wright’s F_ST was 0.368 (95% C.I.=[0.332,0.407]) for barley and 0.301 (95% C.I.=[0.270,0.333]) for wild barley. Among population diversity at quantitative traits calculated as Spitze’s Q_ST ranged from 0.283 to 0.774 in barley and 0.221 to 0.703 in wild barley. Both species have similar values of diversity. However, the structure of the diversity is different in populations of cultivated and wild barley. Additionally, there is a wide range of Q_ST estimations for both species, indicating that different traits have experienced different selection pressures. By comparing the evolutionary history of the different traits in both species, we were able to gain an insight of the relative role of each trait in the domestication process of barley.