Misodendrum comprises eight species of aerial hemiparasites endemic to temperate forests of Chile and Argentina that parasitize Nothofagus. This mistletoe is unique in that it has feathery staminodes on its wind dispersed achenes. Previous classifications included two subgenera, Misodendrum (two sections) and Angelopogon (three sections). The present study tested this classification using two chloroplast genes (trnL-F and matK) and 31 morphological characters. Maximum parsimony, likelihood and Bayesian analyses were performed for individual and combined partitions. Results from analyses of the separate partitions differed only in the positions of M. linearifolium and M. quadriflorum; however, the 2-gene tree gave higher support for M. quadriflorum as sister to all other species. Misodendrum brachystachyum and M. oblongifolium form a well supported clade that is sister to one composed of M. punctulatum, M. gayanum, and M. angulatum. These phylogenetic relationships generally agree with previous taxonomic classifications. Subgenus Misodendrum, characterized by warty stems and two stamens, here resolves as a polytomy: M. punctulatum, M. gayanum, and M. angulatum. Subgenus Angelopogon, characterized by the plesiomorphies three stamens and foliacious bracts, is paraphyletic given our rooting. Misodendrum brachystachyum and M. oblongifolium (section Archiphyllum) differ morphologically only by the length of their fruiting staminodes.