During the examination of a series of specimens, formerly referred to Myotis montivagus, recently collected in Vietnam and Lao PDR, we found that they differ in several important ways from any species formerly included in M. montivagus. We describe them as a new species characterised by a relatively long forearm, moderately long ears, flat cranial profile and wide anteorbital bridge. Based on characters classically used to separate the ‘subgenera’ of Myotis the new species shows affinities to both the nominate subgenus ‘Myotis’ and ‘Selysius’. Our morphological investigations support recent phylogenetic analyses showing that the former ‘subgenera’ of Myotis are in fact paraphyletic groups, even within Southeast Asia. Nevertheless, many of the external and craniodental features formerly used to separate these subgenera provide a practical means of grouping species. Using these characters we provide an identification key to identify the new species, as well as other currently recognized medium and large sized, small-footed Myotis species from the Indomalayan Region.