We examined the phylogeny of the genus Rubus in Korea using an internal transcribed spacer (ITS) of the nuclear ribosomal DNA and a trnL-trnF (trnL/F) intergenic region of the chloroplast DNA. In all, 21 ingroup species (1.2 kb for each species) were analyzed using parsimony, resulting in 672 aligned sequences from ITS, and 502 bases with trnL/F. Individual and combined analysis of ITS and trnL/F data proved that the genus Rubus is a monophyletic group. This phylogeny also substantiated a previous sectional classification scheme rather than a subgenus classification scheme. However, our results did not support the earlier sectional classification by Focke (sect. Corchorifolii), but did support the sectional classification of Nakai: sect. Crataegifolii (R. crataegifolius, R. takesimensis and R. trifidus), and sect. Villosii (R. corchorifolius). Most of these species, which are found in Korea and belong to subg. Idaeobatus, appeared in two different groups in all data sets. This suggests that this subgenus is a polyphyletic group that has gone through at least two independent evolutionary processes. The taxa, when mapped onto the combined tree, showed that the occurrence of their morphological characters of simple and compound leaves was concurrent in Korean Rubus. ITS sequence data were consistent overall with the geographical distribution of each species. Furthermore, the trnL/F sequence data provided phylogenetic information within closely related species.