The patterns of shape variation of the first upper molar and mandible have been investigated within and among wood mice (Apodemus as sex and age of the animals could be a source of within-group morphological variability interfering with among-groups patterns of differentiation. The relative importance of both sources of shape variation was investigated, in order to evaluate the robustness of patterns of fine-scale geographic differentiation. The increasing age of the animals, estimated by wear stages of the upper tooth row, caused significant variations in size and shape of the molars due to progressive abrasion of the cusps. It also involved shape changes of the mandible due to bone remodelling. However, these intrapopulational effects are of limited importance compared to geographic differentiation. Gene flow among populations should be favoured across mainland populations but lowered between mainland and islands, and to a lesser extent among close islands. Shape differences in molars are in agreement with this expected pattern of gene flow. Patterns of mandible differentiation rather match local variations in habitats. At this fine geographic scale, molar shape would vary according to the amount of genetic exchange among populations whereas mandible shape might be under local selective and/or functional constraints.