Phylogenetic analyses of two chloroplast and five putatively unlinked nuclear DNA regions were used to explore the evolutionary relationships of a circumpolar arctic polyploid species complex in Silene. Gene phylogenies inferred from introns in the low copy nuclear genes RPA2, RPB2, RPD2a, and RPD2b, and ITS1 and ITS2 from the nuclear ribosomal DNA region, indicate two consecutive polyploidization events. The first involved the diploid arctic/subarctic S. uralensis lineage as the cytoplasmic donor, as indicated by chloroplast rps16 and psbE-petL sequences, and highly unexpected from a morphological perspective, the diploid Siberian/northeast Asian S. ajanensis lineage as pollen donor. The hybridization and polyploidization resulted in the tetraploid S. involucrata lineage. A second hybridization and polyploidization with the S. ajanensis lineage as pollen donor, and the tetraploid S. involucrata lineage as cytoplasmic donor, resulted in the hexaploid lineages of S. sorensenis and S. ostenfeldii. In general, two paralogous sequences were identified from the tetraploids and three paralogues from the hexaploids in the low copy nuclear genes. Interlocus concerted evolution appears to have homogenized the ITS regions, because only the sequences corresponding to the paternal lineage were recovered in the polyploids. The power, and neccessity, of using several potentially unlinked regions is revealed by the fact that the gene phylogenies had small deviations from the general pattern explained by alloploidy. These deviations are better explained as gene duplication and/or lineage sorting events, or simply lack of information.