The genus Arceuthobium (dwarf mistletoes, Viscaceae) comprises 42 species that parasitize hosts in Pinaceae and Cupressaceae in the Old and New Worlds. Maximum parsimony analyses were conducted on two data partitions (separately and combined): nuclear ribosomal internal transcribed spacer (ITS) sequences for all 42 currently recognized species and chloroplast trnT-L-F sequences for 34 New World species. The Old and New World species were phylogenetically distinct using ITS, thus making subgenus Arceuthobium paraphyletic. Arceuthobium pendens and A. guatemalense comprise the basalmost clade of subgenus Vaginata, characterized by the presence of flabellate secondary branching. The trnT-L-F sequences, which vary widely in length depending upon taxon, contain three times less phylogenetic signal than ITS, although homoplasy for this partition is lower. Several of the clades obtained from analysis of nuclear ITS sequences are also recovered using trnT-L-F sequences such as A. guatemalense and A. pendens, the A. rubrum group, the A. vaginatum group, and the A. campylopodum group. The ITS + trnT-L-F tree is well resolved except for four internal nodes. A revised classification of the genus is discussed that recognizes only monophyletic species that are well differentiated by molecular data.