Before 2001, it was believed that only one mouse-tailed bat species was found in Yemen—the lesser mouse-tailed bat, Rhinopoma hardwickii. In 2001, a paper was published that cited the presence of the small mouse-tailed bat, R. muscatellum, in the Hadramaut Province of Yemen. However, an analysis of mitochondrial DNA in 2007 found a "deep genetic gap" between R. muscatellum in Iran and the individuals identified as R. muscatellum in Yemen. The genetic distance for the two populations was 8–9%. The lineages of the two populations are estimated to have diverged 10 million years ago. The 2007 study concluded that the population discovered in Yemen in 2001 was a distinct clade within R. muscatellum, but the authors stopped short of describing it as a new species. The Yemeni population of R. muscatellum was described as a new species in 2009 based on the genetic difference described in the 2007 paper. Its species name hadramauticum is a Neo-Latin derivation of "Hadramaut", which is the place where the holotype was collected.
