Amphoricarpos Vis. is an early diverging genus within tribe Cardueae (Carduoideae, Asteraceae), which is disjunctly distributed in the Balkan Peninsula, Anatolia and the Caucasus; the Anatolian and Caucasian taxa are sometimes treated as separate genus Alboviodoxa. We focus on the monophyletic Balkan populations, which have been treated very inconsistently in previous taxonomic accounts (one polymorphic species with or without varying sets of intraspecific taxa vs. two species, one of them with two subspecies). In order to disentangle relationships among populations across the entire distribution area of Amphoricarpos on the Balkan Peninsula, we employed amplified fragment length polymorphisms (AFLPs) as well as nuclear and plastid DNA sequences (ITS and rps16-trnK) to a dense sampling of populations. ITS was also used to reconstruct the genus' spatiotemporal evolution. In addition, we contrasted the genetic results with morphological data to provide a sound taxonomic revision of Amphoricarpos on the Balkan Peninsula. The split between the Balkan populations and the Anatolian A. exsul took place in the late Miocene or early Pliocene, whereas diversification within the Balkan lineage is much younger and likely started in the Pleistocene. The deepest splits seen in AFLPs and/or ITS separate the geographically disjunct northern-and southern-most populations. Divergence within the continuous distribution area in the centre is shallower, but allowed recognition of three largely allopatric clusters. Morphometric data, however, were neither in line with previous multi-taxon treatments nor with patterns of genetic divergence. We therefore refrain from recognising any of the genetic groups as a distinct taxonomic entity and rather suggest treating all Balkan populations as a single, genetically, morphologically and ecologi cally variable species, Amphoricarpos neumayerianus (Vis.) Greuter, without intraspecific taxa.