Traditionally the genus Pleurospermum and the related genera Aulacospermum, Hymenidium, Hymenolaena, Physospermopsis, Pseudotrachydium, Pterocyclus, and Trachydium, have been problematic taxa with regard to their circumscription and composition. Pleurospermum s. s. includes one or two closely related boreal species but more than 40 other species, distributed mainly in the Sino-Himalayan floristic area, have been attributed to it by different authors in various classifications. Relationships in this taxonomic group are unclear. A molecular phylogenetic analysis of nuclear (nrITS) and cpDNA (psbA-trnH and trnL-trnF) sequences of representative species of Pleurospermum s. l. and closely related Hymenidium, Aulacospermum, Trachydium, Physospermopsis, Pseudotrachydium, Sinolimprichtia, Pterocyclus, and Hymenolaena (55 species in all) was conducted and compared with an analysis of morphological characters. Only two traditional genera were supported as monophyletic groups in the molecular trees, namely Aulacospermum (including Pseudotrachydium) and Hymenolaena. Two stable groups were revealed within Hymenidium. One group included H. chloroleucum, H. heterosciadium, H. hookeri, and H. delavayi. The second included H. lindleyanum, H. stellatum, H. huzhihaoi, H. wilsonii, and Trachydium roylei. Various species of Hymenidium and Trachydium were scattered throughout the tree. The molecular data did not confirm an early divergence between northern and Sino-Himalayan species of Pleurospermum. This indicates that Pleurospermum s. l. and most of the other genera included in this study are polyphyletic.