This data set describes nuclear microsatellite genotypes derived from twelve autosomal loci (6AB, Aph02, Aph08, Aph19, Aph23, Bca10, Bca11, Hhi5, Sfi11, Smo07, Smo09, and CRG), and two Z-linked microsatellite loci (Bca4 and Smo1). A total of 111 Long-tailed Ducks were examined for this genotyping with samples coming from the two primary breeding locales within Alaska (Arctic Coastal Plain of Alaska and the Yukon Delta, Western Alaska) and a representative locale in the central Canadian Arctic (Queen Maud Gulf Bird Sanctuary, Nunavut, Canada). The sex of most samples was determined in the field by plumage and later confirmed by using the CHD molecular sexing protocol (Griffiths et al., 1998).