The genus Alyssum is one of the largest, yet least known genera of the Brassicaceae family. The present study focusses on the Central European populations of A. montanum, a species that is highly variable with respect to its morphology, ploidy levels and ecological requirements. This variation is naturally reflected in a number of recognised infraspecific taxa, and diverse opinions exist with regards to their value and circumscriptions. Based on amplified fragment length polymorphism (AFLP), as well as morphometric and flow-cytometric evidence, we demonstrate here that the variation patterns contradict the current taxonomic concepts held for this species. Our data support the division of the analysed populations into the following groupings: (i) the ‘core’ group that includes most of the Central European diploid and tetraploid populations; (ii) the diploid ‘Swiss–SW German’ group, also including the population from the type locality of A. montanum; (iii) the hexaploid A. montanum subsp. pluscanescens, a Slovenian and Croatian endemic suggested to be of hybrid origin; and (iv) the diploid ‘Serbian’ group from the sand dunes of Deliblatska Pescara. A. repens, represented by a diploid population from Austria and tetraploid populations from Romania, is confirmed to be distinct from A. montanum. On the other hand, we suggest rejecting the recognition of A. montanum subsp. brymii, an assumed endemic of Slovakia and Hungary, and A. montanum subsp. montanum and subsp. gmelinii in their traditional circumscriptions.