Walterinnesia aegyptia is one of the most venomous snakes belonging to the family Elapidae found in the Middle East and Africa. In addition to its ecological importance, it is accused of millions of deaths due to snakebites. Because molecular identification of snakes is crucial for the antivenom drug industry, mitochondrial genes are used to identify, characterize, and infer genetic diversity among different venomous snake species. Data of Walterinnesia collected from samples across Saudi Arabia were compared based on the mitochondrial 16S and 12S rRNA sequences with other congeners to assess the phylogenetic relationship. The phylogenetic analysis strongly supports the monophyly of the genus Walterinnesia based on two genes that represent different species of Elapidae. In addition, a close relationship between Walterinnesia aegyptia and W. morgani was found. Our molecular data showed that W. morgani from Riyadh, Saudi Arabia, is nearly genetically identical (D=0) with W. aegyptia from Ha`il and Riyadh, Saudi Arabia, and Sinai, Egypt. Further study is required based on more material and detailed morphological and genetic analysis.