The genetic diversity within Ptyodactylus ragazzii was analysed for the first time across the Western part of its range. We have used two mitochondrial (12s rRNA and 16s rRNA) and one nuclear (Cmos) marker to compare results directly with other related Ptyodactylus species, P. oudrii and P. hasselquistii. Results show high levels of intraspecific variability, with at least three divergent mtDNA lineages that have different haplotypes for Cmos and that are geographically concordant. P. ragazzii from Mauritania is probably a distinct species and possibly other lineages too, such as those from the Aïr Mountains in Niger, although more nuclear markers are needed to confirm this. All analysed Ptyodactylus species appear to be cryptic species complexes containing multiple deeply divergent forms, highlighting the need for a careful reassessment of the taxonomy of the whole genus.