We have investigated genetic variability among 56 individuals of the apogamous Dryopteris affinis complex from 9 populations in Switzerland and Austria using inter-simple sequence repeats. Our sample included 6 diploids, 48 triploids, and 1 tetraploid and 1 pentaploid plant each. We found genetic differences between and within the different ploidy levels. All diploids genetically differed from each other. In contrast, among the triploid plants we only found seven different genotypes of which one was rather common. The tetraploid and pentaploid individuals were nested among the diploids and triploids. No hypotheses have yet been proposed to explain the origin of genetic variations such as those documented here. We hope that this study stimulates new ideas about the position and the genetic background of this taxonomically difficult species group, in particular, and of apogamous species complexes in ferns in general.