Tragopogon dubius is one of the most widespread species of Tragopogon, extending across much of Eurasia. Traditionally, T. dubius has been considered a morphologically homogeneous species that includes all Tragopogon collections with yellow flowers and swollen peduncles under capitula. Here we describe a new species of Tragopogon from the Iberian Peninsula, T. lainzii, which has heretofore been included in T. dubius. To this end, we performed comparative morphological, cytogenetic, and molecular analyses on many populations of both species. Our results show that T. dubius is not a homogeneous species and that different lineages exist across its broad geographic distribution. Moreover, we show that hybridization has occurred in the wild between sympatric populations of T. dubius, T. lainzii, and T. porrifolius.