Drought stress is one of the important abiotic stresses in plants and leads to major damage in grain yield as well as plant growing, plant structure, and plant metabolism. Sesame is one of important oilseed plants in warm and semi warm region of Iran and regularly faces with drought stress in planting season. In order to investigate genetic variations of sesame lines for their response against water limitation and role of morphologic traits in such condition as screening markers, this two year experiment was conducted during 2007-2008 in Moghan region of North West of Iran. During the first year, quantitative drought tolerance indices were measured with respect to yield values under normal and drought stress conditions. Indices such as SSI, STI, TOL,and MP were evaluated for 22 genotypes originated from different regions in the world and finally first year results showed that STI and MP were designated as the most efficient indices for drought tolerance evaluation of genotypes. In the second year according to STI, 10 genotypes selected, 5 of which had highest, 3 had medium and 2 had lowest STI values, which were used to assess morphological traits with a Split Plot in the form of Complete Randomized Blocks (CRB) design with three replications. Results indicated that irrigation levels as well as the genotypes differed significantly for all studied traits in both normal and two stress conditions. Likewise, there was a positive significant relation between morphologic traits and grain yield. Also results showed that correlations between STI and morphological traits was positive. In other words results revealed that studied traits react to stress condition therefor these traits could be useful and effective for screening sesame tolerant genotypes. Interestingly, the superior genotypes in this study were all of Iranian origin (Karaj-1 and Oltan) which are recommended as the best genotypes for regions suffering from water limitation as geemplasm for breeding program.