Epigenetic and dental variation was studied in ten populations of the common vole (Microtus arvalis) from the Czech and Slovak Republic. A total of 1,536 specimens were scored for 34 cranial non-metric traits. The dependence on sex, size and correlation between traits was evaluated. The mean measure of divergence was used to express the interpopulation differences. The clustering of population generally agreed with their supposed subspecific status. The revealed epigenetic differentiation was not in concordance with the pattern of occlusal variation of M1 and M3. These results are discussed in respect of estimates of genetic and phenetic differentiation within and among populations.