Most of the molecular taxonomic studies on the Eurasian long-eared bats (Plecotus) are based on mitochondrial data only, which might lead to erroneous assessment of the phylogenetic relationships. Here, the genetic divergence among the Mongolian species of Plecotus is examined using sequences of two nuclear introns (THY and ABHD11) and the mitochondrial cytochrome b gene. Both mitochondrial and nuclear data support the existence of three species: Plecotus ognevi, P. kozlovi, and P. turkmenicus. The status of the latter taxon was unclear, as it was previously known from a single record in Mongolia. In our study, P. turkmenicus is found to be widely distributed across the hyperarid deserts south of the Altai Mountains. In several locations, it is sympatric with P. kozlovi, the distribution of which is associated mostly with the semidesert zone, while P. ognevi occurs in the steppe and forest zones of northern Mongolia. The two desert species (P. kozlovi and P. turkmenicus) are quite similar in their morphology and ecological affinities; however, the molecular data clearly show that P. turkmenicus is highly divergent from both P. kozlovi and P. ognevi. In contrast, the mtDNA difference between the arid-dwelling P. kozlovi and the morphologically distant forest-steppe P. ognevi is low. This result demonstrates that more than one lineage of Plecotus independently developed adaptations to the arid habitats of Central Asia and suggests that the morphological similarity between P. kozlovi and P. turkmenicus is a result of convergence. The difference in mtDNA between the Mongolian and West-Central Asian populations of P. turkmenicus indicates that the former may represent a separate taxon of uncertain rank.