Genetic variation at the melanocortin-1 receptor (MC1R) gene is correlated with melanin color variation in a few reported vertebrates. In Gyrfalcon (Falco rusticolus), plumage color variation exists throughout their arctic and subarctic circumpolar distribution, from white to gray and almost black. Multiple color variants do exist within the majority of populations; however, a few areas (e.g., northern Greenland and Iceland) possess a single color variant. Here, we show that the white/melanic color pattern observed in Gyrfalcons is explained by allelic variation at MC1R. Six nucleotide substitutions in MC1R resulted in 9 alleles that differed in geographic frequency with at least 2 MC1R alleles observed in almost all sampled populations in Greenland, Iceland, Canada, and Alaska. In north Greenland, where white Gyrfalcons predominate, a single MC1R allele was observed at high frequency (>98%), whereas in Iceland, where only gray Gyrfalcons are known to breed, 7 alleles were observed. Of the 6 nucleotide substitutions, 3 resulted in amino acid substitutions, one of which (Val(128)Ile) was perfectly associated with the white/melanic polymorphism. Furthermore, the degree of melanism was correlated with number of MC1R variant alleles, with silver Gyrfalcons all heterozygous and the majority of dark gray individuals homozygous (Ile(128)). These results provide strong support that MC1R is associated with plumage color in this species.