In many arctic-alpine plant groups, reticulate evolutionary histories have resulted in problems with species delimitation and phylogenetic reconstruction. In the Saxifraga rivularis complex (2n = 26, 52), the number of species accepted ranges from a single polymorphic one (S. rivularis s.l.) to several (the circumpolar S. hyperborea, the amphi-Atlantic S. rivularis, the three amphi-Pacific species S. bracteata, S.flexuosa, and S. arctolitoralis, and S. debilis in the Rocky Mountains). A combination of molecular (AFLPs), flow cytometrical, and morphological data from samples covering most of the distribution range was used to delimit taxonomic species and to unravel their evolutionary relationships. Four lineages with distinct morphological differences were recognized, representing four species: the diploids S. bracteata, S. hyperborea (including S.flexuosa), and S. debilis, and the tetraploid S. rivularis (including S. arctolitoralis). Based on a synthesis of the available data we provide a taxonomic revision of the complex and propose one rank change (S. rivularis subsp. arctolitoralis comb. et stat. nov.). Genome sizes as well as the intermediate position of the S. rivularis lineage in the molecular and morphological analyses suggest a single allopolyploid origin from the S. bracteata and the S. hyperborea lineages, most likely in Beringia.