Tragopogon is a large Eurasian genus of approximately 150 species. Despite the use of 6910 aligned bp of sequence data representing seven loci, relationships within the genus remain largely unresolved. The young age of the genus in combination with rapid diversification may be the best explanation for this poor resolution. Our studies have revealed that Geropogon is well supported as the immediate sister to Tragopogon. Sections Tragopogon, Brevirostris, Chromopappus, and Hebecarpus of traditional taxonomic treatments are largely monophyletic; sections Angustissimi, Majores, Collini, and Profundisulcati are non-monophyletic. The monotypic sections Macropogon, Dasypogon, and Dybjanskya appear within other sections and no longer merit recognition. Our molecular investigations of geographically widespread species in Europe, including T. crocifolius, T. pratensis, T. porrifolius, and T. orientalis, indicate that each may be non-monophyletic, comprising several cryptic species. These widespread diploids are the proposed parents of some of the Eurasian allopolyploids, as well as the parents of the recently formed T. mirus and T. miscellus from North America