Section Cochlearia (Brassicaceae) includes highly polymorphic species complexes with regard to ploidal level, ecological adaptation and distribution. Low levels of chloroplast DNA divergence suggest that taxa most likely have diversified relatively recently, and that speciation is still ongoing. This has led to conflicting taxonomic treatments. The European Cochlearia displays a range of ploidal levels, from diploid to decaploid. Diploid species with chromosome number 2n = 12 dominate in southwestern Europe, whereas the arctic Cochlearia is diploid with 2n = 14. In Iceland, diploid plants of both basic numbers (2n =12, 14) are found. Whereas the 2n = 12 plants are found only in beach cliffs along the Icelandic coast, the 2n = 14 plants are found in two different habitats: In snowbeds on inland mountains, and along the western coast of Iceland. There is still no agreement as to which taxa the Icelandic plants belong. It has been suggested that the 2n = 14 plants belong either to the arctic diploid C. groenlandica (2n = 14) or constitute a subspecies of the tetraploid C. officinalis (2n = 24). The 2n = 12 plants have been related either to C. groenlandica or to the southwestern European diploid C. pyrenaica (2n = 12). In this study, single nucleotide polymorphisms (SNPs) derived from RAD-sequencing were applied to study whether the Icelandic Cochlearia plants constitute genetic clusters in accordance with chromosome number or ecology. Additionally, to investigate their evolutionary relation to other Cochlearia species, Icelandic plants were compared to recognized diploid species in Svalbard (C. groenlandica) and southwestern Europe (C. pyrenaica and C. aestuaria). Analyses of SNP data showed that Icelandic plants cluster according to ecology, and not according to chromosome number. Furthermore, the genetic variation among the Icelandic populations display a geographic pattern, where plants sampled in closely located sites are more similar irrespective of chromosome number. Icelandic plants do not cluster with southwestern European plants, but alpine (2n = 14) plants on Iceland consistently group with C. groenlandica in Svalbard. Based on the results from this study, it is suggested to refer alpine Icelandic plants to C. groenlandica. The Icelandic coastal plants show no clear genetic or morphological separation between plants with different chromosome number (2n = 12, 14), and they should therefore be referred to the same taxon. However, because the relation to C. officinalis (2n = 24) was not addressed in this study, it is not decided which taxon they should be referred to.