The harsh desert environment of Saudi Arabia, though seemingly inhospitable, harbours a rich herpetofauna. Field surveys conducted between 2019 and 2024 led to the rediscovery of the Sinai Fan-Toed Gecko (Ptyodactylus guttatus), a species distributed in the countries of southern Levant, previously known in Saudi Arabia only on the basis of a few historical records. This study combines phylogeographic analysis and ecological niche modelling to explore the species' genetic diversity and potential distribution. Phylogenetic analyses revealed four distinct lineages within Saudi Arabia, though nuclear markers showed a degree of allele sharing among these lineages. Ecological niche modelling suggests that the species' range may be nearly twice as large as previously assumed from its entire range, now extending into Tabuk, Medina, Bahah, and Ha'il Provinces of Saudi Arabia, showing a significant range extension. Additionally, by including topotypic material of P. ananjevae, we clarify its status within the P. hasselquistii species complex, laying an essential groundwork for systematic revision within this complex. This study enhances our understanding of herpetofaunal diversity in Saudi Arabia and emphasises the need for continued fieldwork and genetic research.