Clematis, a largely temperate genus of vines and lianas, consists of approximately 300 species. Based on a sampling of about 75 species, sequences of the nrITS, the plastid atpB—rbcL spacer, psbA—trnH—trnQ spacer, and rpoB—trnC spacer regions were analyzed using parsimony, maximum likelihood, and Bayesian inference methods. Analyses of the combined data set by the three methods yielded similar topologies. Previously recognized genera including Archiclematis and Naravelia are nested within Clematis, supporting the merging of these genera within Clematis. Ten major clades with various levels of support were detected in the combined analyses. Our results in general do not support previous infrageneric classifications based on morphological characters and suggest significant convergence in floral and vegetative characters in Clematis. Several clades were resolved as regional geographic groups. Bayesian dating suggests a relatively ancient origin of the genus in the Oligocene, yet a relatively recent species radiation of the crown Clematis in the Miocene. Geologic and climatic changes in the late Tertiary to Quaternary are perhaps important for the speciation of Clematis, especially in eastern Asia. Long-distance dispersal of the fruits by wind, water, and/or animals and strong environmental adaptability, are proposed as the main mechanisms for the current cosmopolitan distribution and high species diversity of Clematis.