AbstractAimArctic plant species are often characterized by a complex genetic structure because of changes in their population size, the fragmentation of metapopulation systems, extensive hybridization and allopolyploidization, and survival in disjunct refugia, historical features associated with Pleistocene glaciation. We assessed the biogeographical and genetic patterns in three closely related northern species of peat‐moss (Sphagnum inexspectatum, S. orientale and S. miyabeanum), especially interspecific hybridization, infraspecific geographical differentiation and Pleistocene survival in one or more refugial areas. We tested alternative hypotheses of refugial survival in three widely disjunct regions: eastern Asia, Alaska and Greenland.LocationNorth America (Canada, western USA and Greenland), China, Japan and Russia.MethodsFour hundred and forty‐three plants were genotyped at 12 microsatellite loci. Nucleotide sequences from 130 accessions for two plastid and two nuclear loci were used to reconstruct haplotype relationships. Population genetic analyses produced estimates of genetic diversity, levels of interspecific gene flow and rates of infraspecific intercontinental migration. Approximate Bayesian computation was used to test alternative biogeographical scenarios.ResultsWe found evidence of hybridization between two of the three species, but phylogenetic patterns are predominantly divergent rather than reticulate. Disjunct populations of one species, S. orientale, in Greenland, Alaska and China are genetically differentiated, but migration has occurred among all three metapopulation systems. Divergence‐time analyses strongly support the hypothesis that S. orientale survived the Last Glacial Maximum in Beringia and also in Greenland.Main conclusionsOur results indicate that Beringia served as a refugium for peat‐mosses, and therefore peatlands, which are currently extensive at high latitudes of the Northern Hemisphere. Sphagnum orientale also appears to have survived the Last Glacial Maximum in Greenland, indicating that the species persisted in multiple Pleistocene refugia. Phylogenetic patterns are relatively simple in these mosses compared with those commonly encountered in Arctic angiosperms.