Abstract Accurate species delimitation is crucial for biodiversity research, as it significantly impacts taxonomy, ecology, and conservation. Recent advances in molecular phylogenetics and integrative taxonomy have improved classifications and resolved long-standing taxonomic uncertainties. Here, we use Hyb-Seq (489 nuclear loci) and phylogenomic approaches to investigate Afrocarduus, a genus endemic to tropical Afromontane and Afroalpine regions. Our analyses reveal 16 evolutionary lineages within this relatively young genus (crown age 2.3 Mya), with new morphological data strongly supporting the recognition of each lineage as a distinct species. We demonstrate that the stemless habit evolved independently in species from the Ethiopian Highlands and the East African Rift System (EARS). Notably, we show that the concept of the stemless Afrocarduus schimperi adopted by the Flora of Tropical East Africa, in fact, comprises seven clearly recognizable species, which we formally reinstate. Unexpectedly, the stemmed Afrocarduus nyassanus was recovered as paraphyletic with Afrocarduus ruwenzoriensis nested within it, probably due to incomplete lineage sorting or hybridization. Additionally, the stemmed Afrocarduus keniensis may represent a complex of cryptic species, and we describe a new stemmed species from southern Ethiopia, Afrocarduus kazmi sp. nov. We expand the number of accepted species in Afrocarduus from eight, as recognized in the Flora of Tropical East Africa, to 18 (including two species for which we were not able to obtain molecular data). Our study thus highlights a substantial prior underestimation of the diversity of Afrocarduus in Afromontane and Afroalpine habitats.