Despite more than 100 years of detailed analysis of morphology and macromolecules, the phylogenetic origin of the Monotropoideae remains unclear. In this study partial sequences from the 28S rRNA gene were used to test two alternative hypotheses: (i) that the Monotropoideae share a most recent common ancestor with the Arbutoideae in the Ericaceae or (ii) that the Monotropoideae is the end result of a gradual transition from autotrophism to mycotrophic parasitism in the Pyrolaceae. Our results support the hypothesis that the Montropoideae and the Arbutoideae are a monophyletic group and that the Monotropoideae should be included in the Ericaceae rather than the Pyrolaceae. The Monotropoid species Pleuricispora fimbriolata could not be placed within either the Monotropoideae or the Arbutoideae with any degree of confidence, leaving open the possibility that the Monotropoideae is polyphyletic.