Anthyllis montana is a submediterranean, herbaceous plant of the southern and central European mountains. The internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were sequenced from multiple accessions of the species and several closely related taxa. In addition, amplified fragment length polymorphism (AFLP) was analysed from 71 individuals of A. montana collected in 20 localities, mainly in the Pyrenees, Alps, Italian Peninsula and Balkans. Our ITS phylogeny showed a sequential branching pattern in A. montana, implying a western Mediterranean origin followed by an eastward migration. ITS clock calibrations suggest that speciation of A. montana took place at the Pliocene–Pleistocene boundary, while intraspecific divergence dates to Late Quaternary times (i.e. 0.7 million years ago). The AFLP analyses revealed a major genetic (west/east) subdivision within A. montana, probably caused by the massive glaciation of the Alps during this latter time period. The present-day absence of A. montana from vast parts of the Alps, which appear ecologically suitable for the species, together with the finding of evenly distributed AFLP variability within each of the two western and eastern lineages identified, is taken as evidence for a largely static Late Quaternary history without large-scale migration. High levels of AFLP variation observed among populations, together with weak or absent patterns of isolation by distance, seem to be in accord with long-term population insularization and distributional stasis. However, recent small-scale migration and a narrow hybrid zone between western and eastern lineages need to be postulated to explain the intermediate genetic composition of individuals from the Maritime Alps, a well-known suture-zone for other plant and animal species.