DNA sequences from the nuclear ribosomal ITS and from the chloroplast trnL-trnF regions of 47 species of all six subgenera and 13 sections of Saussurea were analysed. The cladogram resulting from ITS sequence data indicates that Saussurea in its present circumscription is paraphyletic. S. sect. Elatae and S. subg. Jurinocera together are sister to the genus Jurinea. The affinities of S. subg. Frolovia are unclear, while representative species of the remaining four subgenera and ten sections form a strongly supported monophyletic group. Within this clade, the delimitation of S. subg. Eriocoryne and S. subg. Amphilaena against S. subg. Saussurea is not evident. The trnL-trnF intergenic spacer sequences show a remarkable synapomorphy, a 21bp insertion, for Jurinea cyanoides, S. deltoidea, S. ceratocarpa and S. frolovii, supporting the paraphyly of Saussurea. These results correspond to differences in morphological characters of achenes and pappus, which also suggest that S. sect. Elatae, S. subg. Jurinocera and S. subg. Frolovia are not closely related to the remainder of the genus. Consequently, S. sect. Elatae is separated as the new genus Himalaiella, and the small generic segregates Frolovia and Lipschitziella are resurrected. A synopsis of these three genera is presented and the new combinations Himalaiella abnormis, H. afghana, H. albescens, H. auriculata, H. chenopodiifolia, H. chitralica, H. deltoidea, H. foliosa, H. heteromalla, H. nivea, H. peguensis, Frolovia frolovii and F. gorbunovae are validated.
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