Traditional Chinese medicine has a long history of using plants therapeutically including multiple species of the genus Rubus (Rosaceae). Fruits and other parts of Rubus plants have had a significant effect on human health and nutrition in both ancient and modern times. The pharmacological effects of Rubus include anti-inflammatory, antibacterial, anti-stress, anti-cancer and anti-aging properties. One of the current challenges limiting further development of Rubus resources in traditional Chinese medicine is a poor understanding of phylogenetic relationships among Rubus species in general and especially among Asian species, and also the need for additional studies of phytochemicals. Several confounding factors are frequent hybridization, polyploidy, and highly variable morphology due in part to diverse ecological conditions across species’ distributions. The goal of this study was to elucidate phylogenetic relationships among Rubus species in the predominantly Asian subgenera Idaeobatus and Malachobatus emphasizing species valued in traditional Chinese medicine. Sequences of six noncoding (plus matK) chloroplast DNA regions totaling 8,276 aligned characters were analyzed for 35 Rubus species using maximum parsimony (MP) and maximum likelihood (ML). Both analytical approaches yielded topologically identical phylogenies except for one additional grouping in the ML tree. The phylogeny has nearly complete resolution and divides the species into two primary clades; one comprises R. geoides (representing the Southern Trans-Pacific clade), R. nivalis (subg. Chamaebatus) and R. trivialis (representing subg. Rubus) and the other is composed largely of R. arcticus and R.saxatilis (subg. Cylactis), and the large subgenera Idaeobatus (raspberries) and Malachobatus. Within the latter, principally Asian clade, three unresolved lineages exist (four using MP) precluding an improved understanding of the relationships among them. However, three major subclades containing Asian species have good support. Two contain subg. Idaeobatus species only, and the third comprises members of the exclusively polyploid subgenera Malachobatus and Dalibardastrum. Examination of the presence of biochemically active terpenes reveal that triterpenes are common among subg. Idaeobatus species with diterpenes reported only in R. pungens and R. chingii (not sampled). Subg. Malachobatus species have not been as thoroughly investigated so triterpenes may also be common in these species. From these results, multiple subg. Idaeobatus and subg. Malachobatus species may be good candidates for terpene analysis as members of their respective clades possess triterpenes. Moreover, five species not currently used in traditional Chinese medicine should be evaluated as they also occur in China, and may possess medicinal value.