Trace elements play crucial roles in various metabolic processes in living cells. Nicotianamine synthase 2 (NAS2) and Vacuolar Iron Transporter 2 (VIT2) genes contribute to Iron (Fe) uptake in plants. These two genes have been studied in various plant species including bread wheat. In this study, we examine the genetic diversity and estimated the putative effects of variants for these two genes among a diverse set (192) of high-yield bread wheat and durum wheat genotypes together with their diploid progenitors T.urartu, A. speltoides, and A. tauschii. Our analyses indicate that both genes have several homoeologs and orthologs/paralogs present across diverse set of wheats, other monocots and the dicot species. We identified 421 and 46 single nucleotide polymorphisms (SNPs) among all genotypes studied in NAS2 and VIT2 genes, respectively. Variant Effect Predictions indicated that about 15% and 19% of these variants were predicted as putatively deleterious (SIFT £ 0.05) and tolerated (SIFT 3 0.05) mutations in NAS2, while 4% of tolerated mutations were identified for VIT2 gene. Further analysis has identified about 26 and 7 haplotype groups for NAS2 and VIT2 genes, respectively, although the maximum number of haplotype groups were observed for diploid wheats. However, the total haplotype diversity and effective migrant rate were higher for VIT2 as compared to NAS2. These results highlight that both transporter genes have been under independent selection and the haplotypes and SNPs identified within the exonic region of these genes could be useful to manipulate the Fe uptake and homeostasis in crop plants.