Classification of Rhododendron species based on morphology has led to a consensus taxonomy recognizing the major subgenera Azaleastrum, Hymenanthes, Pentanthera, Rhododendron, Tsutsusi, and three minor ones. To determine whether these subgenera are monophyletic and to infer phylogenetic relationships between Rhododendron sections and species, we carried out a cladistic analysis using molecular data, including all groups within the genus. For this purpose, we sequenced a large part of the nuclear gene RPB2-I, encoding a major RNA Polymerase II subunit, from 87 species and analyzed the data by maximum parsimony, maximum likelihood, and Bayesian methods. The resulting phylogenies show subgenera Azaleastrum and Pentanthera to be polyphyletic and group all Rhododendron species (except the two in section Therorhodion) into three large clades. Based upon these results, modifications in Rhododendron classification are proposed, which consolidate minor subgenera and recognize monophyletic subgenera and sections.