The genus Neomys contains four species, three of which are present on the Iberian Peninsula. Recent phylogeographic studies have thoroughly assessed the evolutionary history of this genus in this region. However, perhaps due to its rarity, the isolated and endangered populations of southern Iberia have never been included in these studies. Thus, the current taxonomic status of these apparently isolated populations of Neomys anomalus is currently based on morphological evidence. In order to test whether southern Iberian Neomys represent a recently diverged relict population from recent expansions of previously described phylogroups, or a highly divergent lineage due to isolation in an ancient southern refugia, we genetically analyze four museum individuals of Neomys anomalus from this southern population in Andalucia, Spain. Our results based on cytochrome b sequences from two individuals suggest that the southern Iberian Neomys population represents a relatively recently diverged lineage with a unique haplotype. This is in contrast to other phylogeographic studies on Iberian small mammals. These findings might suggest potential recent extinctions throughout the species' southern range and/or the need for additional sampling in this region in order to properly assess the distribution and conservation status of this Iberian endemic species.