The genus Microthlaspi comprises several morphologically weakly differentiated species. The species are highly diverged regarding their ploidy levels and are usually summarised under the designation Thlaspi perfoliatum agg. The diploid members of the species complex, M. granatense, M. umbellatum and M. natolicum, are distributed in Northwest Africa, Southeast Spain and Turkey with neighbouring areas. Microthlaspi perfoliatum is more widely distributed all over Europe and shows three ploidy levels. Diploid M. perfoliatum is restricted to Middle Europe whereas polyploid M, perfoliatum is distributed all over Europe and related areas. Individual plants from 106 natural populations throughout the geographic range were analysed using isozyme analyses. In correlation with the corresponding ploidy level polymorphisms in molecular data partition populations of M. perfoliatum geographically and reflect ancient speciation processes as well as postglacial Vegetation history. We characterized nine loci combining 38 alleles. Within polyploid M. perfoliatum the allele number is greatly increased. Diploid taxa are ancestral in phylogenetic analysis. Moreover, polyploid M, perfoliatum combines alleles from two diploids, M. perfoliatum and M. natolicum, and there is great evidence of multiple evolution of polyploid M. perfoliatum.