Abstract Vespertilionidae is a species-rich family of bats that experienced rapid diversification events and contains many morphologically conserved taxa, resulting in challenges to taxonomic and phylogenetic resolution for members of this family. One example of a challenging group is the pipistrelles, which several studies have recovered as paraphyletic. Pipistrellus nathusii is noteworthy for being recovered either as sister to other European Pipistrellus species, more closely related to Nyctalus, or sister to the clade comprising Nyctalus and European Pipistrellus species. Using a core data set of 6 nuclear introns, and an extended data set of 10 nuclear introns, we employ multiple independent phylogenetic methods that are robust in the presence of incomplete lineage sorting or hybridization to resolve the placement of P. nathusii. In addition, our data confirm the distinction of the Asian Pipistrelle taxa which form a distinct genus sister to the clade comprising Vansonia, Pipistrellus, and Nyctalus.