Two species of Rubus occur naturally in the Hawaiian Islands, R. hawaiensis and R. macraei. It has been previously thought that R. spectabilis, a western North American species, and R. hawaiensis share a recent common ancestor based on morphological similarity, and that R. macraei was a later derivative of R. hawaiensis. DNA sequences of the chloroplast gene ndhF were used to reconstruct the phylogeny of these species with non-Hawaiian members of subgenus Idaeobatus. These findings strongly contradict the previous hypothesis for the origin of the Hawaiian Rubus. Although R. hawaiensis is closely related to R. spectabilis, R. macraei is distantly related to these species. Sequence identity, genetic distance, and phylogenetic analysis all suggest that R. macraei is distantly related to New World and Asian species of subg. Jdaeobatus. Consequently, R. macraei and R. hawaiensis may have arisen from two separate colonizations in the Hawaiian Islands rather than one as previously assumed. The ancestry of R. macraei may trace to other Pacific Rim islands.