Temminck's stint breeds in Eurasian arctic tundra and subarctic and temperate boreal zones in a range extending from Fennoscandia to easternmost Siberia. In contrast to the favourable global conservation status of the species, it has been classified as vulnerable in Finland and near threatened in Sweden. A fragment of the control region of mtDNA was sequenced from 127 individuals from breeding areas in Fennoscandia in the west (three populations) and in the eastern end of the range. The mtDNA variability and structuring were among the lowest values reported for waders (FST −0.02616). The mtDNA sequences revealed seven haplotypes, of which four were present in single individuals. The most common haplotype occurred in 81% of all individuals and in all birds in the Siberian sample. There was evidence of two maternal lineages. The most common lineage occurred in 95% of the individuals and was the only one present in the Siberian sample. The lineages coexisted in all three Fennoscandian populations, indicating a secondary contact of two previously isolated populations. The mtDNA variation and the mitochondrial nucleotide and haplotype diversities indicated panmixis of the populations. However, a higher degree of population differentiation was detected in microsatellite allele frequencies (125 birds, six loci) in Fennoscandia between the Bothnian Bay population and the two inland populations (Lapland and southern Norway). The difference may be caused by the female-biased dispersal pattern of the species. In addition, the Bothnian Bay population appeared to be genetically bottlenecked, an observation in concordance with the recent decimation of the population.