Nuclear DNA sequence variation of the internal transcribed spacer (ITS) and amplified fragment length polymorphisms (AFLPs) were used to illuminate the evolutionary history of Pritzelago alpina, a herbaceous perennial of (sub)alpine to nival habitats of the European high mountains. Maximum likelihood analysis of ITS sequences of P. alpina, Hornungia petraea and Hymenolobus procumbens (the ‘Pritzelago alliance’) resolved P. alpina and H. petraea as sister taxa. ITS divergence estimates support an origin for P. alpina in the Late Tertiary, while intraspecific diversification started in the Late Quaternary (0.4–0.9 million years ago). AFLP analysis of 76 individuals of P. alpina, representing 24 localities across its entire west–east distribution, identified four mountain lineages in Cantabria, the Pyrenees, (south-) western Alps, and northeastern Alps/Tatras/Carpathians. In an analysis of molecular variance (amova), 14.3% of the total variation derived from this separation. However, relationships among these lineages remained unresolved in neighbour-joining and principal co-ordinates analyses, suggesting a population history of near simultaneous vicariance. Comparison with our previous ITS/AFLP study of Anthyllis montana (Fabaceae) indicates that the two co-distributed but altitudinally differentiated plant species exhibit temporally concordant but spatially discordant patterns of genetic variation. Moreover, levels of AFLP divergence were significantly lower in P. alpina than in the submediterranean, lower-elevation A. montana. Together, these data are consistent with a ‘displacement refugia model’, which predicts that European mountain plant species associated with lower- and upper-elevation habitats had a different cycle of range contraction into (long-term) glacial and (short-term) interglacial refugia, respectively.