Myotis muricola is a widespread species covering the Malay Archipelago through the West and East of Wallace’s Line. The genetic analysis, based on partial cytochrome b gene, shows the high genetic variation within M. muricola. The phylogenetic analysis has indicated that M. muricola in the Malay Archipelago are monophyletic. Members of M. muricola Eastern are grouped together independently of M. muricola Western and both groups are distantly related. On the other hand, M. muricola Western and M. muricola Eastern are distinct species and sister taxa to M. mystacinus. Based on the high genetic distance (26.8% to 38.5%) and the Genetic Species Concept (Baker & Bradley, 2006), it can be concluded that M. muricola Western and M. muricola Eastern should be considered as two distinct species. Furthermore, two subgroups within M. muricola Western, namely Sumatra-Asian and Bornean subgroups, are recognised as distinct subspecies (with genetic distance of 5.1% to 10.8%). The evidence from the molecular data indicated M. muricola Eastern as the ancestor of M. muricola species complex in the Malay Archipelago, which had earlier diverged into the western region during the Pliocene. Meanwhile, the geographical conditions during the Pleistocene had given more chances for fauna to diversify. It was predicted that M. muricola diverged in the western part of the Malay Archipelago during the Pleistocene when the sea level dropped and produced some landbridges among the islands in Sundaland. The hypothetical dispersal routes of M. muricola are related to the ancient Sunda River systems that produced gallery forest corridors for migration and which served as Pleistocene refuges during the migration.