Nycteris madagascariensis is an enigmatic bat species, described as endemic to Madagascar and known only from two century-old specimens. Vigorous recent efforts to document this species on the island have proven unsuccessful. We extracted DNA from the fluid-preserved paratype of this taxon and used high-throughput sequencing methods to recover cytochrome b sequence data, which was overlaid on an extensive phylogeny of Afrotropical Nycteris. We also analyzed craniodental measurements of both Malagasy and Afrotropical Nycteris using principal components analysis and one-way ANOVAs. Both genetic and morphological analyses unequivocally place N. madagascariensis in a clade otherwise known only from eastern and coastal Kenya. Review of the collector’s notes and itinerary raises doubts on the accuracy of its having originated in Madagascar; the hypodigm was probably collected during his travels in coastal East Africa. We therefore place Nycteris madagascariensis G. Grandidier, 1937 in the synonymy of N. macrotis sensu lato and remove this species from the bat fauna of Madagascar.