The polymerase chain reaction (PCR)-based amplified fragment length polymorphism (AFLP) technique was applied to elucidate the glacial history of the alpine cushion plant Saponaria pumila in the European Alps. Special emphasis was given to a dense sampling of populations. Our data support a survival of S. pumila during the last ice age in at least three refugia, which are characterized by unique marker sets. Patterns of genetic diversity and divergence can be explained by survival in peripheral refugia and additional in situ survival within the ice sheet on peripheral nunataks. A nunatak survival in interior parts of the Alps needs not be postulated to explain our results. The level of genetic diversity is dramatically different between populations (Shannon's diversity index: 0.87-19.86). Some peripheral populations are characterized by a high number of rare fragments indicating long isolation, but not necessarily by a high level of genetic diversity. Parts of the present distributional area were recolonized via recent long-distance dispersal, leading to severely bottlenecked populations lacking private or rare fragments. The combination of our data with palaeogeological and palaeoclimatological evidence allows us to confine Pleistocene refugia to certain regions and to draw a detailed scenario of the glacial and postglacial history of S. pumila.