Abstract: Our knowledge of species diversity in biodiversity hotspots remains incomplete. The Qinghai-Tibet Plateau (QTP) and the mountainous region of southwestern China have long been regarded as biodiversity hotspots. However, despite considerable efforts, numerous plant species may still elude formal description. Rhodiola L. (Crassulaceae) encompasses ca. 58 perennial herb species, which have been used as an important traditional medicinal plant for centuries. Rampant exploitation has put some species at risk of extinction. Rhodiola has also been recognized as a promising model for investigating radiation speciation in the QTP. However, the phylogenetic relationships among major clades in the genus are still not well resolved, and the underlying causes of cytonuclear discordance briefly mentioned in previous studies remain unexplored. Through phylogenomic analyses utilizing data from both the nuclear genome and plastome of 42 species, we identified six major clades in Rhodiola and found extensive cytonuclear discordance, which was primarily attributed to hybridization and introgression occurring among clades or closely related species. In addition, the integration of morphological, phylogenomic, population genomic, and ecological evidence resulted in the identification and description of a new species of Rhodiola: R. renii sp. nov., and the reclassification of a previously Pseudosedum species merged into Rhodiola. Our results highlight the significant role of hybridization and introgression in the evolution of Rhodiola and probably other rapid‐radiated groups in the QTP, and emphasize the need for increased species discovery efforts in biodiversity hotspots such as the QTP and its adjacent mountainous areas.

Key words: gene flow, incomplete lineage sorting, new species, phylogenomics, Pseudosedum, Rhodiola, the Qinghai-Tibet Plateau