Variability in the coat color of the house mouse, Mus musculus, provides an opportunity to study the evolution of phenotypes in this species. Here we associated genetic variations with coat color in seven mice from Madagascar that had identical M. m. gentilulus mitochondrial DNA sequences. The entire coding region of the 948-base pair (bp) coat-color-related gene, Mc1r, was shown to have no nonsynonymous changes. However, analyses of the two exon-1 promoter regions—termed 1A (317 bp) and 1B (499 bp)—from a second gene, Asip, which is also involved in the evolution of coat color, revealed two distinct haplotypes in each region. Associations between Asip promoter regions and dorsal color were ambiguous; however, two ventral color types—light and dark gray—were associated with the haplotypes of 1A, as determined by clustering analysis. Notably, the haplotype of the light gray animals was identical to the Asip A^w allele that is associated with white bellies.