Horizontal gene transfer (HGT) between sexually unrelated species has recently been documented for higher plants, but mechanistic explanations for HGTs have remained speculative. We show that a parasitic relationship may facilitate HGT between flowering plants. The endophytic parasites Rafflesiaceae are placed in the diverse order Malpighiales. Our multigene phylogenetic analyses of Malpighiales show that mitochrodrial (matR) and nuclear loci (18Sribosomal DNA andPHYC) place Rafflesiaceae in Malpighiales, perhaps near Ochnaceae/Clusiaceae. Mitochondrialnad1B-C, however, groups them within Vitaceae, near their obligate hostTetrastigma. These discordant phylogenetic hypotheses strongly suggest that part of the mitochondrial genome in Rafflesiaceae was acquired via HGT from their hosts.