The Alyssum montanum–A. repens polyploid complex is a group of related perennial taxa with a diversity centre in the European (Sub)Mediterranean, controversial taxonomic treatments, and a poorly known evolutionary history. In the present study, morphological, ploidy level and genetic (AFLPs and chloroplast DNA sequences) data were collected to address the taxonomy and evolution of a sublineage of this complex distributed in southwestern Europe and Morocco. As a result, a new taxonomic treatment, differing substantially from recent concepts, is presented, including an identification key, synonymy and typifications. The recognition of several previously described but recently not accepted endemics is favoured (A. flexicaule, A. orophilum, A. rhodanense), whereas the existence of southern Iberian endemics is not supported. Most of the Iberian Peninsula is occupied by a single species for which the name A. fastigiatum is applicable. Populations from the summit areas of the Pyrenees represent a separate species, which is described here as A. cacuminum. Populations from coastal sand dunes in the Basque country (Bay of Biscay) and Galicia, recently recognised as two subspecies of A. loiseleurii, are elevated to species rank according to their genetic and morphological divergence. Alyssum atlanticum is resolved as a species confined to northern Africa and not reaching southern Spain. The distribution of A. montanum in a strict sense is much more restricted than previously reported, being delimited by the Pyrenees in the south, and the Alps in the northeast. The species complex studied here is composed of several polyploid stenoendemics confined to different mountain ranges or specific lowland habitats, and a few relatively widely distributed species. We infer that hybridisation and polyploidisation events, along with ecological and geographic isolation, have stimulated speciation in this complex. Hypotheses about the origin and evolutionary history of the species are discussed.