The Kuhl's Pipistrelle (Pipistrellus kuhlii) exhibits several deeply divergent mitochondrial lineages across its range. These lineages could represent cryptic species or merely ancient polymorphism, but no nuclear markers have been studied so far to properly assess the taxonomic status of these lineages. We examined here two lineages found in Western Europe, and used both mitochondrial and nuclear markers to measure the gene flow between bats carrying them. The sampling focused on an area of strict sympatry of lineages in Switzerland but also includes bats from North Africa. All individuals were sequenced for the COI gene to identify their mitochondrial lineages and five microsatellite loci were used to cluster them according to their nuclear genotypes. Although they share mitochondrial sequences, all North African genotypes were clearly different from European ones. However, within the area of sympatry in Switzerland only a weak west/east geographic structure was observed. This weak nuclear structure is independent of mitochondrial lineages as bats carrying both variants are completely admixed. Thus, these two divergent lineages do not represent a cryptic taxonomic diversity, but are elements of a single biological species. They are the remnants of a secondary admixture of vicariant subpopulations. We argue that these isolated subpopulations likely undertook a recent bipolar recolonization of areas north of the Alps, as both molecular markers and historical records of P. kuhlii are compatible with a spatial expansion during the last decades. These results highlight the need of using appropriate markers before claiming the existence of cryptic species based on highly divergent mitochondrial lineages.