We analyzed the sequences of nuclear ITS and SSU rDNA, and mitochondrial atp1, matR, and LSU and SSU rDNA (total length about 9000 bp) from 13 species and 9 Genera of Rafflesiaceae s.l. Separate and combined phylogenetic analyses of these six data sets gave consistent results. They identified four clades that were previously recognized as Rafflesiaceae s.s., Apodanthaceae, Cytinaceae, and Mitrastemonaceae. Furthermore, based on expanded unpublished analyses with other angiosperms, Mitrastemonaceae do not form a monophyletic group with the other Rafflesiaceae s.l. Bdallophytonforms a clade with Cytinus.

Key words: atp1, matR, mitochondrial LSU and SSU rDNA, nuclear ITS and SSU rDNA, phylogeny, Rafflesiaceae s.l.