We used RAPD markers to study the population genetic structure and diversity of Saxifraga rosacea subsp. sponhemica, a rare Central European endemic rock plant with a highly disjunct distribution. Because of strong isolation current gene flow between populations is very low or absent. However, an isolation by distance pattern of genetic differentiation suggested historical gene flow during the last glaciation when suitable habitats for S. sponhemica were much more abundant. In most populations, considerable genetic variability has been preserved due to the longevity of S. sponhemica. Our results suggest that long-lived plant species can maintain historic genetic patterns despite small size and strong isolation of populations. Several RAPD loci were identified to be non-neutral and their frequencies correlated with climatic gradients, indicating natural selection. Adaptive genetic variation could be important for adaptation to environmental changes like ongoing climate change. The taxon does not appear to be genetically threatened in the short term, but populations are threatened by habitat destruction. The establishment of new populations in suitable habitats with seeds from the same region may be a suitable conservation measure avoiding potential maladaptation due to local adaptation.