To investigate the population genetic structure of the goosander (Mergus merganser) in Europe and to identify populations with a significant conservation value, we isolated nine microsatellite loci, and screened them in the subspecies Mergus merganser merganser and Mergus merganser americanus. All markers were polymorphic with two to 15 alleles per locus. Average observed and expected heterozygosity values were 0.422 and 0.624, respectively, for the European and 0.497 and 0.667, respectively, for the North American subspecies. Only one marker departed significantly from Hardy–Weinberg expectations in both subspecies. This marker was highly variable but homozygous in all females, suggesting a sex-linked inheritance.