Four wheat cultivars, Gemmeiza10, Misr1, Sakha93, and Giza168 were used in this study as well as the hybrids resulted between all the studied four cultivars. Misr1 Sakha93 resulted hybrids were identified using salinity primers Na+/H+ antiporter gene amplification followed by sequencing while Giza168 Gemmeiza10 resulted hybrids were identified by drought primers DREB2 gene amplification followed by sequencing. The resulted sequences were compared with those available on NCBI website database through the BLAST bioinformatics tool. The obtained data showed that, the base size of Na+/H+ antiporter gene was 400 bp while the base size of DREB2 gene was 200 bp. the phylogenetic analysis showed that Na+/H+ antiporter gene obtained sequence was related to four accession numbers from gene bank. In addition, phylogenetic analysis exhibited an amount of genetic change on the root of clades 0.0020, where the Na+/H+ antiporter gene -based phylogeny tree included four clades. The clades grouping had low support (bootstrap value between 6-8%). Also, the obtained DREB2 gene sequences were aligned with six accession numbers in the NCBI website database as shown from the phylogeny tree. The phylogenetic tree deducted from the sequence comparison of DREB2 gene region showed that the length of branch that represents an amount of genetic change of 0.0020, where it's based phylogeny tree included four clades. The clades grouping had low support (bootstrap value between 8-12%).