Abstarct: Response to salinity of 45 genotypes of sesame was investigated through analysis of morphological traits associated mextabolites Iranian breeding lines (Varamin2822, Yekta, Darab1, TN234 and TN240), Asian genotypes (EM, Indian, Iraqi and Pakistani) and their 36 F1s were considered to determine the tolerant versus succeptible genotype. Tests were carried out in hydroponic culture; the control medium was and the saline media contained150 mM NaCl and 200 mM NaCl. Significant differences (p < 0.01) were observed between salinity and control conditions for all the traits under scrutiny. Morphological traits showed a drastic reduction under stress. As expected, leaf proline and proline content increased with salinity. mextabolite isolation was performed on sensitive (Iraqi) and tolerant genotype (Precocious × Pakistani) in both non-saline and saline (200 mM NaCl) conditions. The tolerant genotype more proline, myo-inositol, D-manitol, and sorbitol. Although genotype had some stress responsive mextabolites such as β alanine, L-serine, citric acid, an proline, its different behavior in response to salinity may be due to the absence/ shortage of the main stress-responsive mextabolites. Following mextabolite analysis, the exxpression patterns of some genes, namely pyrroline 5-carboxylate synthetase, inositol monophosphate synthetase and Phenylalanine ammonia 1, that are involved in proline, myo-inositol and benzoic acid were analyzed in both tolerant and susceptible genotypes under the two conditions. According to the results, proline and myo-inositol can be considered as mextabolites involved in stress tolerance in Sesame.