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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. [ABSTRACT FROM AUTHOR]