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European mammals have been the focus of particularly detailed taxonomic studies by traditional morphological methods. However, DNA analyses have the potential to reveal additional, cryptic species. We describe two highly divergent evolutionary lineages within a small Eurasian mammal, the field vole (Microtus agrestis). We show that the two lineages can be detected not only with maternally (mitochondrial DNA), but also with paternally (Y chromosome) and biparentally (X chromosome) inherited DNA sequences. Reciprocal monophyly of all genealogies and their congruent geographical distributions is consistent with reproductive isolation. Our results suggest that the field vole should be reclassified as two separate species.