The evolutionary history of toad species of East-North of Africa and Arabian Peninsula is intricately connected with the complex geological tectonic waves in these regions and may give rise to strictly endemic species. A total of 39 individual species (18 from Egyptian species Sclerophrys regularis and 17 of Sclerophrys arabica and 4 of Duttaphrynus dhufarensis from Saudi Arabia) were investigated and sequenced for D-loop and 12S rRNA fragments of mtDNA (mitochondrial DNA). This study was carried out to study their genetic diversity and phylogeographic evolutionary lineages. Arabian Peninsula species revealed high genetic and haplotype diversity more than African species S. regularis. The neutrality tests negative value of Tajima's D and Fu's Fu for both S. regularis and S. arabica indicating their deviations from neutrality suggesting the recent population expansion after a bottleneck or selective sweep. By contrast, D. dhufarensis showed positive values may be due to the low frequency of polymorphisms and decreased population size or balancing selection. Molecular phylogeny study of tree building using D-loop gene fragment splits each species in a separate clade, but 12S rRNA coding gene fragment splits African species of toads away from the Arabian Peninsula species. Moreover, these results were supported by the absence of gene flow among the African and Arabian Peninsula species which may indicate their different evolutionary lineage. Our results revealed that the Red Sea together with the evolutionary history of the climate in this region may have highly discontinuity effects, which prevented the gene flow and extensive distribution among the Afro-Arabian amphibian species.