In many arctic plant groups, reticulate histories involving hybridization and polyploidization have resulted in problems with species delimitation and phylogeny reconstruction. The Saxifraga rivularis complex is a typical example. Two taxa, S. rivularis and S. hyperborea, have been reported from the arctic archipelago of Svalbard (‘Spitsbergen’), but their delimitation, relationship, and taxonomic status are uncertain. We analyzed variation in chromosome number and DNA content (using flow cytometry), two types of molecular markers (RAPDs and isozymes), and 59 morphological characters along transects in two large, mixed Svalbard populations. We also included presumedly ‘pure’ reference populations from other sites to address whether the tentative taxa are distinct and whether they hybridize in mixed populations. In the random amplified polymorphic DNA (RAPD) analysis, we identified two very distinct groups of multilocus phenotypes, corresponding to the tentative species. These groups also differed in DNA content, chromosome number (S. hyperborea: 2n=ca. 26; S. rivularis: 2n=ca. 52; but endopolyploidy was observed in several plants), some morphological characters, and isozyme phenotypes (with a few exceptions). The cytosolic Gpi locus was duplicated also at the 2n=26 level and fixed heterozygosity was observed in all populations, suggesting that S. hyperborea and S. rivularis may be secondary allotetraploid and allooctoploid, respectively, rather than diploid and tetraploid as traditionally assumed. We conclude that the Svalbard populations represent two distinct species at different ploidal levels and occurring in partly overlapping habitats, and that extensive hybridization presently does not occur between them even in mixed populations. Most molecular markers observed in S. hyperborea formed a subset of the S. rivularis markers, consistent with a hypothesis that S. rivularis is an allopolyploid lineage with the S. hyperborea lineage as one of its progenitors.