Abstract:The internal transcribed sequence of the nuclear ribosomal DNA (nrDNA-ITS) was chosen as the target sequence to resolve the phylogeny of the genus Viola in China. 66 sequences (39 of which were reported for the first time) of 55 ingroup taxa were collected, with Hybanthus concolor and Scyphellandra pierrei as outgroups. Molecular phylogenetic trees strongly supported the monophyly of Sect. Viola, Sect. Diffusae, Sect. Bilobatae and Sect. Vaginatae. The close sister relationship among Subgen. Melanium, Sect. Viola and Sect. Trigonocarpae was revealed, however, the clade of Sect. Trigonocarpae got low support. Subgen. Dischidium was confirmed to have a very close relationship with Subgen. Chamaemelanium by maximum parsimony tree, but the two Sections (Sect. Longicalcaratae and Sect. Brevicalcaratae) under Subgen. Dischidium should be combined together. Phylogenetic trees also showed that Pinnatae should be treated as a subsection under Sect. Adnatae. Besides, the systematic status of V. lucens, V. magnifica, V. dissecta and V. yunnanensis were discussed combining molecular results with morphologic characters.