The snowy owl (Bubo scandiacus) is a nomadic species with a circumpolar distribution. It has recently declined in the western Palearctic and may thus be worthy of special consideration for conservation. We investigated genetic structure in three well separated geographic regions within the snowy owls' breeding range. We sequenced two mitochondrial genes; the control region and cytochrome b, and two Z-chromosome introns; VLDLR-9 and BRM-15. We found no phylogeographic structure among the sampled regions, indicating high levels of gene flow in the recent past and possibly still today. Intra-population diversity did not vary between regions for the control region, but for Cyt b, North American birds had higher haplotype diversity than Scandinavian and eastern Siberian birds. Western Palearctic birds do not seem to be genetically deprived or inbred. Genetic diversity in the snowy owl was not lower than Scandinavian populations of three other owl species: tawny owls (Strix aluco), Tengmalm's owls (Aegolius funereus) and eagle owls (Bubo bubo).