This data set describes nuclear microsatellite genotypes derived from eight autosomal loci (BCA6, BCA9, BCA11, BCA5, CRG, OXY13, TSP1.20.09 and TSP1.20.46) and a 366 base pair portion of the mitochondrial control region. A total of 665 Greater White-fronted Geese were examined by genotyping and 518 by sequencing with samples coming from its circumpolar range representing multiple flyways (Midcontinent, Pacific, Greenland, Palearctic). The sex of most samples was determined in the field by morphology or cloacal examination.