Salinity stress adversely affects wheat growth and grain yield by altering the expression of particular genes. To identify salinity-tolerance screening markers, we analyzed phenological, morpho-physiological, and biochemical traits, as well as six abscisic acid-related genes, in a salt-susceptible (Saji) and a salt-tolerant (Yavarous) durum wheat cultivar under salinity stress conditions (250 mM NaCl). Significant genetic diversity was observed between the cultivars for all traits. According to the results, increasing phenological traits, including day to maturity, showed a significant negative correlation with grain yield per plant (GYPP). The traits most strongly associated with GYPP were excised leaf water loss (ELWL) with a negative regression coefficient, grain water use efficiency (GWUE), catalase activity, and the K+/Na+ ratio. Regarding yield components, grain weight per main spike, 1000-grain weight, grain number per main spike, and grain number per plant can be suggested as desirable markers for selecting salt-tolerant genotypes. Selection for increasing the traits of GWUE, ELWR, RWC, total chlorophyll, and total carotenoids, and decreasing ELWL and the chlorophyll A/B ratio, were suggested as favorable physiological markers. Among biochemical traits, increased antioxidant enzyme activity, K+/Na+ ratio, Mg2+/Na+ ratio, proline accumulation, total protein, total leaf sugar, total phenol, and flavonoid content, as well as reduced malondialdehyde and hydrogen peroxide levels, can be proposed as selective salt-tolerance markers. According to the results, the expression of genes involved in the abscisic acid biosynthesis and signaling pathways was higher in the salt-susceptible cultivar Saji than in the salt-tolerant cultivar Yavarous under salinity stress. It might be stated that salt-susceptible cultivars rely primarily on rapid gene activation, while salt-tolerant cultivars benefit from preexisting molecular defenses. We believe that the identified markers and the proposed cultivars could be used as favorable indicators and donor parents in future wheat breeding programs.