Rhododendron L. taxonomy has been tested in recent times by molecular phylogenies based on several DNA regions. Most of these studies have aimed at higher-level relationships, despite the importance of lower ranks, such as sections, to most workers on the genus. Almost one-third of the species of Rhododendron are placed in one of the lepidote (scaly) sections, section Vireya (Blume) Copel.f. Results of phylogenetic analyses of the ITS region (ITS-1, 5.8S and ITS-2) for the genus Rhododendron, with sampling concentrated on section Vireya, are presented. The results of Bayesian and parsimony analyses were predominantly congruent. Subgenus Rhododendron is inferred to be monophyletic, while two of the three sections, Rhododendron and Vireya, are polyphyletic; the monophyly of section Pogonanthum Aitch. & Hemsl. was not tested in this study. Relationships between the species of section Vireya do not correspond to the traditional classification based on morphology, instead correlating strongly with geographic areas, with a disjunction between an Australian–New Guinea clade and clades of west and middle Malesian taxa. The phylogeny also indicates that the ITS region may not undergo complete homogenisation in all species of Rhododendron.