In a circumpolar wader, the dunlin (Calidris alpina), there are 11 named subspecies, but only five mitochondrial DNA (mtDNA) lineages have been found. In the present study, we investigated the genetic structure of dunlins in western Palearctic (from East Greenland to Taimyr peninsula) using DNA microsatellites and amplified fragment length polymorphism (AFLP) markers that may detect more recent differentiation than mtDNA. In this region, we consider four described subspecies; alpina, schinzii, arctica and centralis, together comprising two mtDNA lineages. We analyse seven polymorphic microsatellite loci and 91 AFLP markers in 287 and 152 unrelated individuals, respectively, originating from 17 populations. Neither microsatellites nor AFLPs reveal distinct groups that correspond to currently recognized subspecies. There is a clear pattern of isolation by distance in microsatellites. Our results do not contradict the former mtDNA results that there are two phylogenetic lineages (approximately corresponding to schinzii and centralis) that have met and formed a cline (alpina). We find no difference between schinzii and arctica (East Greenland). We conclude that, given the lack of distinct groups and the gradual changes in microsatellite allele frequencies, these markers provide little genetic support for the dunlin subspecies taxonomy in the western Palearctic. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92, 713–726.