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Voles from the Genus Microtus are rodents with a subterranean lifestyle. Central Italy is populated by two species of the Genus, the North-Western Microtus savii and the South-Eastern endemic Microtus brachycercus. Although morphometric features able to help distinguish M. savii from M. brachycercus are lacking, a peculiar morphology of the anterior end of the first lower molar is typical, but not exclusive, of M. brachycercus. Since some skulls with a compatible dental morphology were collected from Long-eared owl pellets in Umbria (Central Italy), a genetic assessment was deemed necessary to verify the possible presence of M. brachycercus outside of its known distribution range. Hemimandibles were isolated and used for both genetic and morphometric dental analyses. Despite the fact that this could suggest the presence of a M. brachycercus population, genetic analyses confirmed the species attribution to the M. savii complex, showing peculiar genetic polymorphisms that can either be due to the wide sampling area, represented by the owls’ hunting grounds, or to the recent evolutive history of the analysed population. This study, once again, underlines the importance of integrative taxonomy, suggesting the key role of predators as field-assistants to minimize the impact of sampling campaign on natural populations.