There is a long-standing debate about the fate of the mountain flora of the European Alps during the Pleistocene ice ages. Two main scenarios of glacial survival of alpine plant taxa have been discussed, namely (1) total extinction within glaciated areas, survival in peripheral refugia, and postglacial re-immigration into vacant areas (tabula rasa hypothesis), and (2) long-term in situ survival within glaciated regions in isolated ice-free areas above the ice-shield (nunatak hypothesis). Four alpine species with differing distributions and ecological demands were investigated to elucidate their glacial history using molecular methods (AFLPs, RFLPs of cpDNA, RAPDs). Their glacial histories are very diverse. Whereas in situ survival in the most intensely glaciated Central Alps played an important role in Eritrichium nanum, the low alpine Erinus alpinus survived in situ on some mountains of the northern Swiss Prealps, and Rumex nivalis grows at intermediate alpine elevations in snow-beds in both the northern and the Central Swiss Alps. In the common arctic-alpine Saxifraga oppositifolia, the species with the widest distribution and ecological amplitude as compared to the other three species, it is not possible to reconstruct its glacial history. It is probable, therefore, that in the Alps, as in northern Europe, resident genotypes surviving glaciation in situ were integrated into the gene pool of postglacially immigrating periglacial individuals. The size of refugia differed according to species and region. On the one hand, refugia were restricted to individual mountains (E. alpinus, R. nivalis). On the other hand, they spanned several mountain ranges in larger areas (E. nanum, E. alpinus). Postglacial migration over longer distances was inferred for E. alpinus from southern France to northern Switzerland, and, over shorter distances, for R. nivalis from the northern Prealps into the Central Alps in Switzerland. Both postglacial immigration and in situ survival shaped the phylogeography at least of E. alpinus and R. nivalis. It is likely, therefore, that the nunatak and the tabula rasa hypotheses are too simplistic to describe the rich diversity of glacial and postglacial processes in Alpine plant species. It rather appears that the glacial history of each species is to a certain degree unique and influenced by its ecological demands or breeding systems. Moreover, stochasticity has to be regarded of essential importance, since factors such as preglacial distribution patterns or postglacial dispersal or extinction events should have had effects on the present genetic composition and the distribution of a species.