Quedenfeldtia (Boettger, 1883) is a genus of diurnal geckos, endemic to the Atlas Mountains in Morocco, with two species being recognized: Quedenfeldtia moerens and Quedenfeldtia trachyblepharus. Quedenfeldtia moerens is found across a wide variety of habitats, from sea level to 3000 m a.s.l., whereas Q. trachyblepharus occupies exclusively high mountain regions reaching up to 4000 m a.s.l. This differentiation, offers an interesting model for study biogeographical patterns and evolutionary scenarios in a North African endemic. Analysis of two mitochondrial (12S rRNA and ND4) and four nuclear (ACM4, MC1R, PDC, and Rag1) DNA markers revealed high genetic variation, consistent with other recent phylogeographical studies, and with the two currently described species. However, within each species, a subdivision into two groups with geographical consistence was found. Multivariate morphological analyses confirmed the existence of two main phenotypes, whereas ecological niche modelling identified various environmental variables associated with the distribution of each species, and helped to predict occurrences outside the confirmed ranges. The results obtained in the present study indicate the possible existence of additional ‘cryptic’ species within this genus, a condition found in many North African reptiles, and particularly common in geckos. In general, North African montane fauna appears to reflect the occurrence of diverse palaeoendemics, as seen in Central Africa Mountain systems, rather than the pattern of recent postglacial recolonization observed in Europe. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ••, ••–••.