Six wheat genotypes which included two lines named by Line-1 and Line-2 in addition to four cultivars (Masr-1, Shandaweel-1, Giza-171 and Sakha-94)) were used in this study.To evaluate the salt tolerant genes in the studied wheat genotypes, 13 SSR markers were applied. Three (10%) were monomorphic, 26 (86%) were polymorphic, and one (3.34%) produced no results. A total of 37 alleles were detected using 30 polymorphic markers. The polymorphic information content (PIC), which found in a range of 0.00 to 0.38 on average, was applied to assess each SSR locus's capacity to differentiate between different wheat cultivars. The significant genetic heterogeneity of wheat genotypes was revealed by cluster analysis. Using salinity primers, amplification of antiporter gene, and sequencing, the six genotypes were specified. Applying the BLAST bioinformatics programe, the sequences were compared with those from the NCBI online database. According to the results, the base size of the salinity-tolerant gene is 200 bp, compared to 600 bp for the antiporter gene(OM200013). The phylogenetic analysis showed that the sequence of the antiporter gene was nearly typical to four gene bank accession numbers. The antiporter gene-based phylogeny tree grouping four clades, and phylogenetic analysis revealed 0.01 of genetic deviation at the root of each clade. As the bootstrap value between 6 and 8 %, the support for the clades grouping was low. Moreover, as can be shown from the phylogenetic tree, the detected salinity-tolerant gene sequences were aligned with four different NCBI website accession codes.