Patterns in the spatial or temporal distribution of genotypes may be indicative of natural selection. Previous work on the woolly mammoth melanocortin-1 receptor ( Mc1r) gene identified three polymorphic positions that suggest Pleistocene populations may have harboured both light- and dark-haired mammoths ( Rompler et al., 2006, 313: 62). Here, we extend this work and present the first population-level analysis of a functional gene in an extinct species. We genotyped the Mc1r gene in 47 woolly mammoth samples excavated from sites across the central portion of the woolly mammoths' former range to examine the extent of variation of this polymorphism through time and across space. Only one individual was found to be heterozygous, indicating that the frequency of the 'light' mutant allele was very low. We conclude that light-coloured woolly mammoths would have been very rare, and may even have been non-existent if the 'light' mutant allele was strongly selected against in its homozygotic form. With the increasing availability of large-scale sequencing technologies, population-level datasets capable of identifying local adaptation will become increasingly attainable.