The polyploid series of Centaurea toletana comprises diploid, tetraploid, and hexaploid cytotypes. Previous studies suggested that the tetraploid was an autopolyploid, while the hexaploid was an allopolyploid and should be considered a different species, C. argecillensis. Sequencing of the ITS and rps4-trnT-trnL, ycf3-trnS, and rpL16 regions, and extensive cloning and sequencing of the ETS region have revealed that many diploid individuals and populations show different ribotypes, likely resulting from ancient hybridization events. Ribotypes found in the diploid populations are also present in tetraploid populations. The extreme difficulties in classifying the tetraploid as auto- or allopolyploid are discussed. The hexaploid C. argecillensis also shows many different ribotypes, including a ribotype not found in the diploids and making an autopolyploid origin unlikely. The pattern of introgression and gene flow implicates several species from the Iberian Peninsula and the High Atlas Mountains in Morocco as genetic donors in ancient hybridization events. This long-reaching network of hybridization may trace its origin to the climatic history of the western Mediterranean during the Neogene.