• atpB–rbcL spacer;
  • ITS;
  • matK;
  • molecular phylogeny;
  • psbA–trnH–trnQ spacer;
  • rapid radiation;
  • rbcL–accD spacer;
  • rpoB–trnC spacer;
  • structural rearrangements

Phylogenetic relationships within Clematis, including Naravelia, Archiclematis and Clematopsis, were analysed using nucleotide sequences of chloroplast DNA [(1) matK and trnK introns; (2) atpBrbcL spacer; (3) rpoBtrnC spacer; (4) psbAtrnHtrnQ spacer; (5) rbcLaccD spacer] and the nuclear ITS regions. The phylogenetic trees resulting from these analyses suggested nine major clades. The genera Archiclematis, Naravelia and Clematopsis were found to be nested within the genus Clematis, and should be included within it. Within the genus Clematis, the traditional subgenus Viorna was found to be monophyletic. The remaining subgenera (Flammula, Clematis and Campanella) and sections Flammula, Clematis and Cheiropsis, however, were found to be paraphyletic or polyphyletic. Recircumscription of several groups in Clematis was suggested. Enormous morphological diversification and very few nucleotide substitutions within Clematis indicate the recent radiation of the genus. Clematidinae shares a gene order with Anemoninae between the starting point of large single copy region and trnQ of chloroplast DNA, although Hepatica, a genus in Anemoninae, shows a different order in the region near trnH. © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society, 2006, 152, 153–168.