Salinity stress is one of the most destructive environmental stresses that considerably reduces wheat growth, development, and productivity. In wheat, like other crop plants, wild relatives have an important role in enriching the genetic background of modern cultivars. Aegilops species possessing the D genome harbor the ideal gene pool for discovering breeding potential. In this study, the effects of different salinity treatments (150 and 200 mM NaCl) on several physiological traits and expression pattern of several genes in three Aegilops species including Ae. tauschii (DD genome), Ae. cylindrica (CCDD genome), and Ae. crassa (MMDD genome) along with a local salt-tolerant bread wheat cultivar (T. aestivum cv. Barzegar) were investigated. Based on results, salinity treatments significantly decreased root and shoot dry weights (RDW and SDW), the relative chlorophyll content, maximum primary (Fv/Fo) and quantum (Fv/Fm) yields of photochemistry of PS II, photosynthesis rate (Pn), root and shoot K+ contents (RK and SK), and root and shoot K:Na ratios (RKN and SKN). In contrast, initial fluorescence (Fo), root and shoot Na+ contents, and the relative expression of SOS1, SOS2, SOS3, HKT, and NHX genes significantly increased due to salinity stress treatments. As a remarkable result, root and shoot dry weights had a positive and strong association with Fv/Fm, Fv/Fo, RKN, SKN, and expression of SOS and NHX genes. In conclusion, our results indicated that Ae. crassa responded well to different salinity treatments than others; thus it could be a candidate for further investigations with an emphasis on using it in breeding programs as an ideal genetic resource to improve salinity tolerance.