Phylogeography has contributed considerably to our understanding of factors influencing population structure and species divergence. We assessed the phylogenetic structure of the widely distributed lacertid lizard Acanthodactylus boskianus, collected for this study from the Fayoum Depression in Egypt, using partial mitochondrial DNA (12S rRNA and ND4). We analyzed specimens of A. boskianus from the Fayoum Depression and compared the genetic content to gene bank-retrieved data for the South Sinai Peninsula and Siwa Oasis. The phylogenetic results indicated two isolated geographic lineages. We suggested that the divergence observed in this phylogenetic study was probably due to the geographical and physical barrier represented by the Nile River, which could have been responsible for a vicariant event producing divergent populations east and west of the Nile. Environmental factors were also discussed here.