Wheat is the most important staple food that acts as a primary source of dietary calories, protein and most of the bioavailable micronutrients such as iron (Fe) and zinc (Zn) for the world’s population. Understanding genetic control of micronutrients uptake is necessary for development of good quality wheat genotypes. To study the nature of inheritance of Zn and Fe efficient uptake under none-saline and saline conditions, two Iranian facultative wheat variety; Navid (salt sensitive, Fe and Zn-deficient) and Roshan (salt tolerant, Fe and Zn-efficient); were crossed to generate six basic generations for generation mean analysis. All the genotypes of these six generations were evaluated for grain Zn and Fe content, agronomic and biochemical traits under none-saline and saline conditions. For all the studied traits, the non-additive components were greater than the additive component. Additive effects were negative and significant for all traits under non-saline and saline conditions, except for 100-SW in control, MDA in 100 mM salinity level, EL and LeaNaC in all salinity levels. Additive gene actions were important for grain Zn and Fe content; while for rest of traits both fixable and non-fixable genetic effects were important. Duplicate dominant type of epistasis was involved in inheritance of all the traits. Broad-sense heritability values (>0.6) for most traits under non-saline and saline conditions were high, whereas the narrow-sense heritability values for most of the studied traits were low to moderate. These Zn and Fe efficient uptake indices could be used to select Zn/Fe-efficient wheat genotypes from segregating populations.