Alyssum montanum ssp. montanum and A. montanum ssp. gmelinii have been treated as two largely sympatric taxa that occur throughout the European continent, the former growing on calcareous and serpentine rocks and in dry grasslands, and the latter mostly on sand dunes. In this study, we demonstrate that the traditional delimitation of these two subspecies is not substantiated and should be considerably revised. Focusing on Central Europe (encompassing the type localities of both names) and inferring from genetic (plastid DNA sequences and amplified fragment length polymorphism markers) and morphological data, we provide here a new circumscription of these two subspecies of A. montanum. The name A. montanum ssp. montanum is applicable to populations in south-western Germany, Switzerland and eastern France, characterized by wider petals and denser leaf indumentum. Alyssum montanum ssp. gmelinii includes diploid and tetraploid populations that are widespread in the rest of Central Europe. Habitat specificity was not confirmed by our studies. The subspecies are allopatric in Central Europe, but their overall distribution ranges in Europe need to be explored further. Genetic patterns suggest different evolutionary histories for the two subspecies. An identification key and a nomenclatural survey are also presented. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169, 378–402.