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The taxonomy of Gerbillus, the most speciose gerbil genus, is highly debated. Of particular contention is the relationship of Dipodillus to Gerbillus; some consider it to be a closely related genus, while others synonymize it with Gerbillus-either with or without recognizing it as a subgenus. The main objective of this study is to test the validity of common taxonomic groupings within the Gerbillus-Dipodillus species complex, which was achieved by using geometric morphometrics to examine cranial and mandibular variation in 34 out of the 52 Gerbillus-Dipodillus species. Craniomandibular size and shape were highly correlated, indicating strong allometric patterns in shape variation. The common taxonomic groups were significantly different in craniomandibular size and shape, yet they did overlap considerably in morphospace. A notable exception was the extreme divergence of Monodia (G. mauritaniae) from all other species in the occlusal view of the mandible. Morphospace overlap is likely a consequence of both phylogenetic history and environmental adaptation. Only the ventral cranium was associated with climate, particularly in areas related to resource acquisition. Geographic distance was not significantly associated with craniomandibular morphometric distance, and the groups overlapped greatly in their geographic range. Cranial and mandibular regions differed in discrimination power-the ventral cranium had among the highest, while the dorsal cranium and the occlusal mandible had the lowest. Craniomandibular regions varied in association with climate, phylogeny, and size-previous studies suggest this difference may be a consequence of different genetic controls for shape variation.