All parasites are thought to have evolved from free-living ancestors. However, the ancestral conditions facilitating the shift to parasitism are unclear, particularly in plants because the phylogenetic position of many parasites is unknown. This is especially true for Rafflesia, an endophytic holoparasite that produces the largest flowers in the world and has defied confident phylogenetic placement since its discovery >180 years ago. Here we present results of a phylogenetic analysis of 95 species of seed plants designed to infer the position of Rafflesia in an evolutionary context using the mitochondrial gene matR (1,806 aligned base pairs). Overall, the estimated phylogenetic tree is highly congruent with independent analyses and provides a strongly supported placement of Rafflesia with the order Malpighiales, which includes poinsettias, violets, and passionflowers. Furthermore, the phylogenetic placement of Mitrastema, another enigmatic, holoparasitic angiosperm with the order Ericales (which includes blueberries and persimmons), was obtained with these data. Although traditionally classified together, Rafflesia and Mitrastema are only distantly related, implying that their endoparasitic habits result from convergent evolution. Our results indicate that the previous significant difficulties associated with phylogenetic placement of holoparasitic plants may be overcome by using mitochondrial DNA so that a broader understanding of the origins and evolution of parasitism may emerge.