Saussurea is one of the largest genera of Asteraceae tribe Cardueae, comprising about 460 species from the Northern Hemisphere with most species distributed on the Qinghai-Tibetan Plateau (QTP) and adjacent areas. A well-supported phylogenetic framework was established based on whole chloroplast genomes of 126 taxa of Saussurea and 14 additional Cardueae taxa analyzed with Bayesian inference and Maximum Likelihood. Our results, however, are inconsistent with previous subgeneric classification of Saussurea on the whole. Some groups shown certain relationships: subgenus Eriocoryne was almost completely delimited, and subgenus Theodorea, subgenus Saussurea section Laguranthera and section Rosulascentes appear closely related. Molecular dating and biogeographic analysis suggest that Saussurea originated in Hengduan Mountains about 18.54 Mya and rapid diversification in this area and a dispersal northwards took place since then in several migration patterns. The barrier effect of QTP might the main reason for the origin especially for the diversification of Saussurea. Both continuous uplift of the QTP and global cooling since mid-Miocene played important roles in the geographic expansion and diffusion; the later, especially, accelerated northward dispersal.

The subtribe Saussureinae is a highly speciose group with more than 600 species distributed in the Northern Hemisphere and is particularly species‐rich at the high mountains of central and eastern Asia. Saussurea and Jurinea are the two main genera described within the subtribe. However, up to 15 satellite genera are recognized in some recent taxonomic treatments with an analytical viewpoint. For the first time, we carried out a complete sampling to clarify generic boundaries based on a well‐resolved phylogeny of Saussureinae. We employed a Hyb‐Seq technique that targets 1061 nuclear conserved ortholog loci designed for Compositae. After a filtering of potential paralogs, 588 loci were retained to infer phylogenetic trees under concatenation and coalescence approaches. High branch support resolution was recovered at the generic level, but a non‐monophyletic pattern was detected for most of the genera as they are currently circumscribed. Accordingly, we propose a new generic delimitation based on the three main clades recovered in the backbone tree, which are also in agreement with morphological evidence: Dolomiaea, Saussurea, and Jurinea. Following this classification into three genera, 18 new combinations are proposed. This new genus delineation will be used as a basis for future evolutionary studies in the Saussureinae.