We examined, in the context of phylogeny, variations in ventral cranial shape in Martino's vole (Dinaromys bogdanovi), a rare rodent endemic to the western Balkans. Our analysis was based on 138 complete adult skulls, which were pooled into 3 phylogeographic groups (Northwestern, Central, and Southeastern). These groups were retrieved in an earlier study based on a 555–base-pair fragment of mitochondrial cytochrome b gene, which suggested a stepping-stone pattern of southward expansion followed by allopatry. Ventral skull shape was analyzed with geometric morphometrics using 23 two-dimensional landmarks. The primary shape differences across groups are the sizes of the auditory bulla and the foramen magnum, the length of the incisive foramen, and the width of the rostrum. Consistent geographic trends in shape changes were rare, and size was stable across phylogeographic groups. Morphological relationships among groups closely resemble genetic distances, implying their neutral evolution rate. We suggest that the adaptive zone occupied by Martino's vole imposes narrow limits to its phenotypic variation. Under the strong pressures of stabilizing selection for the normative (intermediate) phenotype, random drift in isolated populations produced only minor deviations in the ventral cranium.