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The genus Desmodillus is monospecific, consisting of only the Cape short-eared gerbil (Desmodillus auricularis). Despite being widely distributed across southern Africa, previous studies did not find evidence of intraspecific phenotypic geographic differentiation. The objectives of this study is to use geometric morphometrics to investigate if and how the skull of D. auricularis varies spatially. It examines the covariation of skull morphology with broad spatial (latitude and longitude) and climatic variables, based on a sample of 580 specimens from southern Africa (Botswana, Namibia, and South Africa). The results did not support the differentiation of D. auricularis populations into distinct geographically isolated phenotypic groups. However, there is strong evidence for clinal variation in skull morphology; the most prominent pattern being a decrease in size from the west (closest to the South Atlantic coast) to the east (towards the continent's interior). Shape variation was not localized in any skull region and seem to be driven mostly by size (allometry), although it also covaried significantly with latitude and longitude. Statistically significant skull shape sexual dimorphism was also detected, with males having larger crania than females. Spatial clinal variation in skull morphology was mostly associated with differences in the aridity of the habitats relative to their distance from the coast as evidenced by precipitation-related bioclimatic variables—annual precipitation (BIO12), precipitation of driest month (BIO14), and precipitation of driest quarter (BIO17)—covarying the most with skull morphology. This could be driven by either the climate influencing local resources available to populations or by the climate directly instigating phenotypic climatic adaptations. [ABSTRACT FROM AUTHOR]