Soil and water salinity limits the production potential of crop plants in large areas of the world. Due to our arid and semi-arid climate conditions and prolonged irrigation, Iran will be subjected to progressive salinity in the future. Hence, breeding for salinity tolerance of crop plants including staple crops such as wheat, is important. Exploitation of genetic diversity for salinity tolerance present in wild relatives of wheat can be considered as one of the efficient strategies. Aegilops cylindrica species is one of the valuable gene pool of wheat for salinity-tolerance mechanisms such as Na + exclusion. This study was conducted to evaluate the effect of salinity stress on agro-physiological traits using 88 genotypes of Aegilops cylindrica . The genotypes were grown under normal and salinity stress (300mM NaCl) conditions using split plot design with randomized complete block design in greenhouse at Isfahan University of Technology, Iran in 2013-14. Physiological and morphological traits including proline, carbohydrate, malondialdehyde, H 2 O 2 , relative water content, Na + , K + , Ca 2+ concentrations of leaves and roots, K + /Na + , Ca 2+ /Na + ratio, electrical conductivity of leaves and roots, plant and root wet and dry weight, root/shoot ratio, plant height, root length and salinity tolerance index were measured. The results of analysis of variance showed that salinity stress significantly affected all the measured traits. Salinity stress caused significant increases in carbohydrate, proline, hydrogen-peroxide, malondialdehyde content, Na + , Ca 2+ concentrations of root and leaves, electrical conductivity of leaves and roots, and root/shoot ratio while it led to significant decreased in the remaining traits. There were significant differences among Aegilops cylindrica genotypes for all of the measured traits. Under both conditions, positive and significant correlations were observed between K + /Na + ratio and plant dry weigh. Negative and significant correlations were observed between H 2 O 2 content and relative water content as well as proline content and between root wet weight and Na + concentrations under normal conditions. Negative and significant correlations were observed between Na + concentration and plant dry weight, K + concentration as well as between carbohydrates content and Na + concentration, malondialdehyde content, between H 2 O 2 content and plant wet weight, between proline content and K + /Na + ratio and between K + , Ca 2+ concentrations and Na + concentration of root under salinity stress conditions. The results of principle component analysis (PCA) showed the three first components justified 63.22 and 69.82 percent of total variations in normal and salinity stress conditions, respectively. On the basis of bi-plot, genotypes with highest first component (dry matter potential) and lowest second component (Na + uptake potential) had higher tolerance than other genotypes. According to cluster analysis, the genotypes were separated into three groups on the basis of physiological and morphological traits under normal and salinity stress conditions respectively. Groups one to three comprised 35, 28 and 25 genotypes in normal conditions and 26, 52 and 10 genotypes in salinity stress conditions. Overall, genotype number 44 possessed the highest wet and dry plant weight, salinity tolerance indices as well as the lowest electrolyte leakage of leaves, Na + concentration of roots and leaves and also highest first principle component and lowest second principle component under salinity stress, and thus detected as the most tolerant genotype and suggested to be used in future wheat breeding programs. Key word: Salinity stress, Aegilops cylindrica , Physiological traits, Wheat breeding.