We undertook a comparative phylogeographic study using molecular, morphological and morphometric approaches to address systematic issues in bats of the Kerivoula hardwickii complex in Asia. Our phylogenetic reconstructions using DNA sequences of two mitochondrial and seven nuclear genes reveal a distinct clade containing four small-sized species (K. hardwickii sensu stricto, K. depressa, K. furva and Kerivoula sp. nov.) previously assigned to K. hardwickii sensu lato, as well as K. kachinensis, a distinctly larger taxon. Among the four small species, morphological analyses showed that K. hardwickii s.str. differs significantly from the other three species in skull shape, whereas K. depressa, K. furva and the new species appear to be morphologically cryptic species. Molecular dating estimates suggest that species within the hardwickii-complex diversified during the Late Pliocene/Early Pleistocene period, most probably in different glacial refugia in Asia. Available evidence indicates that allopatric speciation within the complex included morphological, acoustic, and cytogenetic divergence, although these were not always mutually exclusive. Such adaptive changes would explain how different taxa with overlapping morphological features can share ecological niches and maintain their gene flow in sympatry. Accordingly, we also suggest that two subspecies of K. hardwickii sensu lato (K. h. crypta and K. h. malpasi) originally described as distinct species (from Southern India and Sri Lanka, respectively) can be re-elevated to species rank. Should these be found to be conspecific however, the name crypta would have priority and malpasi should be treated as its subspecies.