The white-backed woodpecker is a highly endangered species in Sweden, with only three fragmented populations comprising a total of some ten breeding pairs. Restocking with birds from other viable populations may help to overcome the acute situation currently faced, but prior to such an exercise more information about the genetic structure and variability in donor and acceptor populations is required. We developed a set of highly polymorphic microsatellite markers from the genome of the white-backed woodpecker, and genotyped these in Swedish, Norwegian, Latvian and Polish populations to address the genetic status of populations. Marker heterozygosity was not dramatically lower than that seen for other avian species, and was also rather similar between the different populations under study. The number of different alleles was however lower in the small eastern Sweden population, than in the others. Genetic substructuring between populations was generally not pronounced, but individuals from eastern Sweden tended to be more similar to each other, than to birds from other populations. Absence of strong evidence for substructuring may be a consequence of the relatively few number of individuals and markers available for analysis, but we also discuss the possibility of gene flow occurring before the recent population fragmentation, or still existing migrants between the different populations.