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Deserts and arid regions are perceived to have low biological and genetic diversity, which has partially influenced the identification of psammophilic species, especially taxonomic inferences based on morphology alone. Recent studies of Dipus sagitta have revealed clear, deep genetic divergence beyond the species level within this monotypic genus. To clarify the taxonomy of Dipus, we examined a morphometric dataset consisting of 191 voucher specimens covering nearly the entire distribution of the genus to explore skull variation using traditional morphological measurements and geometric morphometric analysis. Phylogenetic relationships within Dipus using two mitochondrial genes (n=383) and six nuclear genes (n=106) were assessed by Bayesian inference and maximum-likelihood procedures. We used a candidate species approach with the divergent mtDNA phylogenetic groups and subspecies identified in previous studies as the starting point and analysed the candidates using five species delimitation methods and two validation methods. Our findings indicate that Dipus can be divided into four phylogenetic groups that include two species: the Deasyi group (D.deasyi), Sagitta group, Sowerbyi group and Turanicus group (D.sagitta). According to the morphological analyses and the examined specimens, pelage colour varies significantly with season and age, making it unsuitable as a diagnostic characteristic of the subspecies. Furthermore, measurements of body size and skull size require a large number of specimens to reach statistical significance and obtain reliable results. Geographical distributions should be considered first when identifying species or subspecies due to the disjunct habitats of Dipus. Our molecular analyses revealed the long-neglected potential diversity in arid regions and improved the efficiency of species/subspecies identification. We also found that individuals from more humid areas or higher altitudes were larger, whereas individuals from drier areas possessed longer appendages and larger tympanic bulla.