In order to clarify the origin of the wide-spread tetraploid Leucanthemum ircutianum and the hexaploid L. adustum, both found in the alpine and dealpine parts of central Europe together with the diploid L. vulgare, we carried out a genetic analysis based on the distribution of amplified fragment length polymorphism (AFLP) fragments in populations of these three taxa, both in the northwestern Alps (Allgäu region, south Germany and adjacent parts of Austria) and the Franconian Jura (vicinity of Regensburg, Bavaria, Germany). Statistical analyses based on AFLP fragments (principal co-ordinate analysis, PCoA; analysis of molecular variance, AMOVA; Bayesian analysis of population structure, BAPS) suggest that neither of the polyploids is of autopolyploid origin based on L. vulgare, but rather are allopolyploids with the second (maternal) diploid parent still unknown.