Generation mean analysis for salt tolerance in wheat was studied on P₁, P₂, F₁, F₂, BC₁ and BC₂ populations of three crosses. The cross-1 was between the salt tolerant Sakha-8 and sensitive Sham-8, cross-2 was between two salt tolerant varieties (Sakha-8 x Line-6) while cross-3 was between salt tolerant Line-6 and sensitive Sham-8. The genotypes were evaluated under control (0.0 mM NaCl) and salinity stress (150.0 mM NaCl) at germination and seedling stage for seven traits. The model of additive/dominance is inadequate for explaining the inheritance of all traits in control and salinity treatments in three crosses. The presence of epistasis in addition to the predominance of non-additive gene effects for all traits except SL indicated that the conventional selection procedure may not be effective enough to improve them. Therefore postponement of plant selection in later generations or the crosses between the selected segregants followed by selfing can be suggested to accumulate alleles favorable for the improvement of these traits. The molecular markers analysis revealed that only four SRAP primer combinations, three TRAP primer combinations and three SSR primer pairs generated polymorphic bands form the tested genotypes. The five polymorphic bands SRAP-2_570bp, SRAP-3_760bp, TRAP-1_205bp, TRAP-3_450bp and SSR-2_215bp appeared only in the tolerant genotypes. These markers may be considered as specific markers for salt tolerance. The identified markers in this study would allow implementation of marker-assisted selection to screen wheat segregating populations for salt tolerance.