We studied phenotypic relationships among six European Apodemus species (A. agrarius, A. epimelas, A. flavicollis, A. sylvaticus, A. uralensis, and A. alpicola) using landmark based morphometrics. Cartesian coordinates of 14 landmarks were recorded on the occlusal projection of upper molars from 175 specimens. Results revealed A. agrarius as the most distinct, having long and slender molars. Since primitive members of the genus (A. atavus, A. orientalis, A. dominans) are characterised by broad and robust molars, we conclude that A. agrarius is the most derived in this respect. Within the Sylvaemus subgenus/species group A. epimelas differed from the remaining four species in having more robust molars and a relatively longer second molar. Within the remaining four species two clusters emerged, although differences between them were slight. The flavicollis-sylvaticus tandem exhibited a relatively shorter second molar and more robust first molar. In five Sylvaemus, the robustness of molars correlated negatively with molar size, suggesting that between-species differences in molar shape result from allometric relations.