Abstract Species of the Thomomys subgenera of pocket gophers dig tunnels differentially; Thomomys are mainly claw-diggers while Megascapheus are tooth-diggers. Specific skull analyses could help in differentiating species in the bottae–umbrinus complex. This study revealed that Megascapheus shows similarity in cranium morphometry but that rostrum shape should show modifications associated with tooth-digging habits. We analysed cranium variation between Megascapheus species to identify interspecific variation. The variation in cranial morphometry within and between eight Megascapheus species was quantified through a two-dimensional geometric morphometry analysis based on 19 dorsal and 19 lateral reference points of 1172 specimens from different localities. Sample shape diversity and discrimination were analysed using principal component analysis (PCA) and canonical variable analysis (CVA). Sexual dimorphism tests were performed on cranium shape and size. A Student’s t-test was performed to explore differences between groups previously evaluated by CVA. PCA revealed considerable overlap across species in terms of view and sexes, with significant differences in Procrustes distances (shape) and centroid distances (size). The analyses showed that species in the subgenus Megascapheus have two main cranium morphotypes associated with the ecosystem that they inhabit. The analyses contribute to confirm the species level for T. fulvus and T. nigricans.