Using a geometric morphometrics approach, we examined shape and size variations of skull and mandible bone of two evolutionarily distantly related mice from Turkey: Mus domesticus and Mus macedonicus. PCA analyses revealed overlap in dorsal cranium and mandible shapes of both species, consistent with previous traditional morphological methods. The skull of M. macedonicus seems to be larger in size than M. domesticus according to box-plot analyses of centroid size values, however there is no obvious difference for the mandible. No difference was observed between sexes in either of the characters. We suggest that future studies focus on dental characteristics and also consider the variation among local populations and ecological variables.