Many species of Stephania Lour. are used traditionally in South-east Asia as medicinal plants. Understanding and predicting their therapeutic properties could be improved, provided that the evolutionary relationships among lineages are clarified. We present the first molecular phylogeny of the genus Stephania, focusing on the species occurring in China on the basis of nuclear (internal transcribed spacer, ITS) and chloroplast (trnL–F) markers sequenced from 29 species of Stephania. Our results showed that S. subgenus Stephania and S. subgenus Tuberiphania are not monophyletic, owing to the phylogenetic placement of a single species (S. mashanica). The relationships with the third subgenus, S. subgenus Botryodiscia, are not resolved. None of the sections in our analyses is monophyletic. Our study calls for further phylogenetic investigations including more accessions from the whole distribution area of the genus. A taxonomic revision of the genus Stephania, which would reassess the appropriateness of the macromorphological characters used so far to distinguish among subgenera (e.g. flower merism, size and aspect of the rootstock and main root), and sections (e.g. inflorescence morphology, sessiliflorous or not), is much needed.