Karyological variation, reproductive isolation, morphological differentiation and geographic distribution of the cytotypes of Centaurea phrygia were investigated in Central Europe. Occurrence of two dominant cytotypes, diploid (2n = 22) and tetraploid (2n = 44), was confirmed and additionally triploid, pentaploid and hexaploid ploidy levels identified using flow cytometry. Allozyme variation as well as morphological and genome size data suggest an autopolyploid origin of the tetraploids. Crossing experiments and flow cytometric screening of mixed populations revealed strong reproductive isolation of the cytotypes. Multivariate morphometric analysis revealed significant differentiation between the cytotypes in several morphological characters (pappus length, length and colour of appendages on involucral bracts, involucre width). The cytotypes have a parapatric distribution with only a small contact zone: diploids occupy the whole of the Central and North European geographic range of the species except for the major part of the Western Carpathians, whereas tetraploids are confined to the Western Carpathians and adjacent areas, both cytotypes co-occurring only in a limited area of intra-montane basins of the Western Carpathians. Based on this array of data, taxonomic treatment of the cytotypes as autonomous species is proposed. The name Centaurea phrygia is applied to the diploids and the name C. erdneri belongs to the tetraploids; nomenclature of hybrids with C. jacea is also resolved.