Two conflicting hypotheses concern the origin of flying mammals. The traditional hypothesis states that the two major groups of bats, the microchiropterans and the megachiropterans, are sister groups that constitute the taxon Chiroptera. In contrast, the diphyly hypothesis suggests that megachiropterans are more closely related to primates than to microchiropterans. Different suites of morphological characters provide support for each of these hypotheses, and previous molecular studies have not provided a clear resolution of the problem. We analyzed a region of the mitochondrial 12S ribosomal RNA gene from 11 species of mammals, including 2 species of megachiropterans, 2 species of microchiropterans, a primate, a colugo (Dermoptera), a tree shrew (Scandentia), and 4 outgroups, to test the diphyly hypothesis. A phylogenetic analysis of 257 base pairs resulted in two shortest unrooted trees that significantly support the monophyly of the bats and also suggest that the colugo is more closely related to primates than to the bats: (((Primates, Dermoptera) Scandentia) (Microchiroptera, Megachiroptera)). The topology supporting the diphyly hypothesis is 10 steps longer than the most-parsimonious unrooted tree. Although the traditional hypothesis is supported with respect to bat monophyly, the rDNA data support the nontraditional grouping of colugo and primates (a hypothesis also supported by neurological data).