The purple saxifrages, Saxifraga section Porphyrion subsection Oppositifoliae, comprise the closest relatives of the arctic-alpine model plant S. oppositifolia and have a centre of diversity in the central and southern European mountain ranges. Many taxa have been described and taxonomic concepts vary among different treatments. Using amplified fragment length polymorphism (AFLP) fingerprinting, we show that some taxa form strongly supported genetic entities best recognized at the species level (S. biflora, S. blepharophylla, S. retusa, S. rudolphiana and S. speciosa), whereas others (S. murithiana and S. paradoxa) are not genetically divergent at all. Saxifraga oppositifolia s.s. is phylogenetically incoherent. Plastid DNA sequence data show limited congruence with the predominantly nuclear-derived AFLPs. Several co-distributed taxa (S. biflora, S. blepharophylla, S. oppositifolia s.s. and S. retusa) share the same set of haplotypes. In the widespread S. oppositifolia and S. retusa, highly divergent haplotype lineages were discovered which exhibit a geographical rather than taxonomic structure. Recent and ancient hybridization and/or lineage sorting are probably responsible for the strong incongruence between data derived from nuclear and plastid genomes. Hybridization, which is known to occur among almost all taxa of this group when growing in sympatry, however, seems to be insufficient to break down species barriers.