Phylogenetic relationships among three species of the genus Apodemus (A. flavicollis, A. sylvaticus and A. agrarius) from seven different localities in Serbia were estimated using arbitrarily primed PCR (AP-PCR) profiling, which allowed clear distinction between the sibling species A. flavicollis and A. sylvaticus. Eight oligonucleotide primers out of the 22 screened, gained a total of 397 amplified bands. The average pairwise genetic distances within Apodemus species ranged from 0.51 between A. flavicollis and A. sylvaticus, to 0.74 between A. sylvaticus and A. agrarius. The large genetic distances obtained among populations of A. flavicollis (0.13) indicate that this part of the Balkan Peninsula was probably a refuge during the last glaciation. Furthermore, differences obtained between populations south and north from the river Danube suggest that this species survived the Last Glacial Maximum in at least two separate refuges. Although our data for molecular markers are from a limited number of localities, extended analyses of C-band distribution on chromosomes from previously studied localities south of the rivers Danube and Sava, indicate that distribution of A. sylvaticus is limited to northern Serbia. Therefore, it is possible that this part of the Balkan Peninsula was not a refuge for this species during the last glaciation.