Apodemus sylvaticus stankovici, described from the topographically rough landscape of the western Balkan glacial refugium, was recently proposed as being either a junior synonym of Apodemus flavicollis or a species on its own right. To untangle this taxonomic vagueness, we sequenced complete cytochrome b gene in 28 field mice collected at 12 locations in the mountains of Bosnia and Herzegovina, Montenegro, western Macedonia and northern Greece. Samples yielded 27 new haplotypes which clustered into two distinct groups. One of these clades also included the reference haplotype of A. flavicollis, while another cluster emerged as being identical with the reference sample for A. sylvaticus. As is common in Apodemus, both species retrieved in our analysis were characterized by low levels of intraspecific variation (0.4–0.9%) as opposed to a high level of differentiation between them (8.0–10.0%); therefore, the taxonomic classification of our material was without doubt. We found no evidence regarding the presence of an additional cryptic species in the mountains of the western Balkans. The very similar values of genetic variability in the two species imply their common evolutionary history of a long-term coexistence in the western Balkan refugium.
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