Variation in the cranium, mandible, and upper molars across eight Apodemus species from the Western Palaearctic, A. agrarius (subgenus Apodemus), A. alpicola, A. flavicollis, A. sylvaticus, A. uralensis, A. witherbyi (subgenus Sylvaemus), and A. epimelas and A. mystacinus (subgenus Karstomys) is compared to molecular divergence. For the first time in this genus, molecular phylogeny is inferred from mitochondrial and nuclear loci using a multispecies coalescent approach. Also for the first time, all three structures are analysed using geometric morphometric methods within a single study and tested for the presence of phylogenetic signal. Our findings indicate that for each morphological structure analysed, A. mystacinus and A. epimelas have the highest mean centroid size values, whereas A. uralensis has the lowestsize variation among Apodemus species aligns with thermoregulatory expectations, although this remains a plausible rather than confirmed explanation due to the absence of direct test against temperature. The most distinctive mandible shapes are observed in A. alpicola and the subgenera Apodemus and Karstomys. Karstomys and A. alpicola also exhibit the most unique cranial morphology, while A. agrarius is characteriszed by its distinct molar shape. Phylogenetic signal is observed in the size and shape variation of each morphological structure analyszed, with the exception of cranial shape, supporting a mosaic model of morphological evolution in Apodemus. The subdivision into the three Apodemus subgenera is consistent only by molar shape, suggesting that molar morphology can serve as a reliable proxy for phylogenetic divergence and thus can be used to clarify phylogenetic relationships within the genus, particularly for fossil material where genetic data are unavailable.