The internal transcribed spacers (ITS) of the nuclear ribosomal DNA and trnL‐F region of the chloroplast DNA were sequenced for all ten species of Chloranthus and the outgroup Sarcandra (Chloranthaceae). Parsimony analyses of separate and combined data sets strongly suggest that Chloranthus is monophyletic and can be divided into two major clades: one containing C. erectus, C. spicatus, C. serratus, C. henryi, C. sessilifolius, and C. oldhamii (Clade A), and the other comprising C. angustifolius, C. fortunei, C. nervosus, and C. japonicus (Clade B). Taxonomically, these two clades correspond to Bentham and Hooker's sections Euchloranthus and Tricercandra. Within Clade A, two subclades, corresponding to Solms‐Laubach's sections Triandri and Brachyuri, can be recognized. Solms‐Laubach's subgenera Fruticosi and Herbacei, however, were resolved as paraphyletic, and thus the traditional division of Chloranthus on the basis of growth habit was not supported. Evidence from ITS and trnL‐F sequences, in agreement with morphology, anatomy, and cytology, strongly suggest that Chloranthus consists of two groups that morphologically may be distinguished by their androecial characters. The present study also supports the hypothesis that the tripartite androecium of Chloranthus may have arisen by splitting of a single stamen with two marginal thecae.