Abstract Harpy fruit bats, two closely related species in the genus Harpyionycteris (Chiroptera: Pteropodidae), exhibit a suite of unique craniodental traits. For this reason, the affinities of these bats have remained unclear, and most systematists have placed them in a group of their own (Harpyionycterinae Miller, 1907). The multicuspidate pattern of the cheek teeth in Harpyionycteris has generated speculation that it may represent an ancestral tribosphenic pattern lost in other pteropodids. In this contribution we propose a phylogenetic placement of Harpyionycteris based on parsimony analysis of complete sequences from two coding genes, the nuclear vWF (exon 28) and the mitochondrial cytochrome b (cyt-b). Both datasets, independently and in combination, strongly support a close relationship between Harpyionycteris and Dobsonia, as originally proposed by Andersen (1912, Catalogue of Chiroptera, British Museum Trustees). In turn, this group nests deeply inside Pteropodidae but it is not closely related to any particular suprageneric clade. Based on other data, we postulate that Aproteles also belongs in this group and therefore propose the expansion of Harpyionycterinae to include Harpyionycteris, Aproteles, and Dobsonia. Regarding the dentition, our results strongly reject the tribosphenic hypothesis advanced by some authors. The multicuspidate cheek tooth pattern seen in Harpyionycteris appears uniquely derived and related to specialized feeding habits and it thus has no direct bearing on the evolution of the typical pteropodid dentition from the tribosphenic pattern of microchiropterans and other mammals.