The delimitation of taxa in the Saxifraga rivularis complex is controversial. In the checklist for the Pan-Arctic Flora, the complex was tentatively divided into five species: the circumpolar S. hyperborea, the amphi-Atlantic S. rivularis and three amphi-Pacific taxa (S. bracteata, S. flexuosa and S. arctolitoralis). Two ploidal levels (2n = 26, 52) are known, indicating a possible history of reticulate evolution. In the present study, a combined approach using molecular (AFLP; 42 populations, 119 plants), ploidal (flow cytometry; 43 populations, 71 plants) and morphometric (81 populations, 216 plants) data were used to identify evolutionary lineages within the complex, and to delimit taxonomic species. Three distinct evolutionary lineages were identified in all analyses of the AFLP data: the Saxifraga bracteata lineage, the S. flexuosa/hyperborea lineage and the S. arctolitoralis/rivularis lineage. The three lineages had different DNA ratios: 0.20-0.21, 0.16-0.17 and 0.36-0.38, respectively. The DNA ratios in combination with the intermediate position of the S. arctolitoralis/rivularis lineage between the two others in multivariate analysis of both genetic and morphological data, suggest an allopolyploid origin of this lineage, with the other two lineages as progenitors. No single morphological character included in this study unambiguously separated among the lineages. They were, however, differentiated by combinations of characters, thus the lineages should be recognised at species level: Saxifraga bracteata, S. hyperborea (including S. flexuosa) and S. rivularis (including S. arctolitoralis). Within the Saxifraga flexuosa/hyperborea lineage two genetical groups were identified, correlating with geography rather than the morphological pattern giving rise to the current taxonomic treatment. The groups may reflect genetical differentiation in glacial refugia through the last glaciation, but are not yet reflected in morphological differentiation, and a division into two taxa is therefore not supported. In the S. arctolitoralis/rivularis lineage, the separation of a Beringian population representing S. arctolitoralis from the Atlantic populations in AFLP data and morphology and the very distant geographical range suggest a subspecific ranking of S. arctolitoralis. Most of the variation within the S. rivularis complex is found in North Pacific areas. This, in combination with the proposed connection to S. bracteata, suggests a Beringian origin for the S. arctolitoralis/rivularis lineage with a later expansion to Atlantic areas.