We used DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) region and the chloroplast trnK intron, including the matK gene, to test monophyly and infer phylogenetic relationships of Rubus and its subgenera. Our ITS and trnK data sets include 17 species representing eight of the 12 Rubus subgenera, Dalibarda repens, and using Fallugia as an outgroup. Separate and combined parsimony analyses suggest that Rubus is paraphyletic because Dalibarda nests within it although bootstrap support is low. A clade including 12 of the species (excluding Dalibarda repens, Rubus pedatus, R. chamaemorus, R. deliciosus, and R. odoratus) is apparent in both the ITS and trnK analyses, and gains strong support (95%) in the combined analysis. This suggests that unarmed and primarily herbaceous, simple-leaved species are ancestral in Rubus. Within the clade of 12 species, several relationships are well supported in both separate and combined analyses. One includes four species of North American blackberries (subgenus Rubus) and another is the relationship between R. crataegifolius of subg. Idaeobatus and R. trifidus of subg. Anoplobatus. These results indicate that subg. Anoplobatus is polyphyletic because R. trifidus is more closely related to R. crataegifolius than to R. odoratus + R. deliciosus which form part of the basal complex in Rubus.

Key words: ITS, phylogeny, Rosaceae, Rubus, systematics, trnK