Bread wheat (Triticum aestivum L., 2n=6X=42, AABBDD) is the most widely cultivated and consumed food corp; regarded as a major conduit towards addressing the food security challenges of 2050. Over the recent years, salt stress (salinity) has emerged as one of the most significant abiotic stress impeding the expansion of wheat cultivation area and posing a threat to international food security. Synthetic hexaploid wheats (SHW) produced from crossing tetraploid durum wheat Triticum turgidum (AABB, 2n=28) to Aegilops tauschii Coss. (DD, 2n=14) provides a unique opportunity for exploiting novel genetic variability for wheat improvement associated with biotic and abiotic stresses. Here the focus was to comprehend the role of diverse Ae. tauschii accessions in SHWs derived from same durum/different Ae. tauschii accessions. While a major objective was to analyze the influence of D-genome on salinity tolerance in these SHWs and their derivatives on the basis of morpho-physiological, molecular and yield related traits against salt tolerance. In this study 136 wheat genotypes were used. Laboratory screening of the seedling salinity tolerance was studied at 0mM, 75mM and 150mM NaCl in Petri plates. After germination, seedling were harvested and data were recorded for shoot length, root length, shoot fresh and dry weight, and root dry weight. Mean square values obtained from analysis of variance showed significant variation for all the recorded observation among wheat genotypes grown under different salt concentrations. Twenty-one genotypes performed best at seedling stage and showed salt tolerance on the basis of biomass production when exposed to 75mM and 150mM NaCl with stress tolerance index ranged from 70-100%. All genotypes were screened at vegetative and maturity stage in greenhouse under control (0mM NaCl) and salt stress (150mM) condition for various morphological, physiological and yield related traits. Analysis of variance (ANOVA) showed that Genotype × treatment interaction expressed highly significant differences for all the observed traits. Multivariate principal component analysis reduced all the traits variables into six and five principle components accounted for 69.64% and 75.76% of contribution to total variation under control and salt stress condition respectively. Correlation analysis showed that sodium ions had strong negative correlation while potassium ions had strong positive correlation with all the recorded observations under salt stress condition. Based on salt tolerant indices of yield related traits i.e. grain per spike, thousand grain weight, grain yield per plant, biological yield and harvest index percentage 41 wheat genotypes were grouped as tolerant, 57 as moderately tolerant, 18 as moderately susceptible and 20 genotypes were grouped as susceptible under salt stress till physiological maturity stage. Forty-eight microsatellite or SSR markers that covered A, B and D genome of wheat were used to characterize the genetic diversity of all genotypes. A total of 208 polymorphic alleles with an average of 4.3 alleles per marker were detected. PIC value ranged from 0.336 to 0.867 with an average value of 0.591 showing considerable genetic diversity among wheat genotypes. Major allele frequency among genotypes ranged from 0.184 to 0.691 with mean value of 0.497. Population structure analysis divided all genotypes into four major subpopulations based on SSR diversity. Association mapping analysis based on 208K SNP sequencing of wheat genotypes identified 528 marker trait associations (MTAs) for various recorded observations under salt stress condition by mixed linear model approach (MLM) with phenotypic variability (R2) ranging from 11.25% to 30.76%. LOD value for various MTAs varied from 3 to 5.68 based on sequencing results. These MTAs covered all the A, B and D- genomes of synthetic wheat and where contribution of the D-genome toward salt stress was shown by 181 MTAs. These MTAs could be utilized in functional characterization of salt related regions and marker assisted selection for better grain yield and grain quality of wheat breeding program in general and of salt tolerance in particular. The overall results indicated that salt stress induces enhanced expressivity of the D-genome and that SHWs is a valuable source of diverse alleles for wide-ranging adaptability and to improve salt stress potential in natural hexaploid wheat.