The hypothesis that color pattern variation in Lake Erie island water snake (Nerodia sipedon) populations results from the opposing effects of natural selection and gene flow requires that this variation have a genetic basis. To determine whether color pattern variation is genetically based, data on the color pattern of wild-caught females and their captive-born offspring were used to estimate heritability of and correlations among four color pattern components. These data, and the results of two laboratory crosses, were also used to test for major locus influences on color pattern. Heritabilities of color pattern components estimated from sib analysis were significantly greater than zero for all four color pattern components, ranging from 0.34 to 0.79. Phenotypic and genetic correlations among color pattern components were positive, ranging from 0.24 to 0.55 (phenotypic correlations) and from 0.40 to 0.82 (genetic correlations). However, inheritance of color pattern was not strictly quantitative. Rather, a major locus appeared to influence color pattern, with alleles at this locus possibly determining whether snakes had regular (mainland-like) or reduced color patterns. Allele frequencies at this locus may have influenced the rate at which island and mainland water snake populations initially differentiated from each other, and may explain the lack of reduced-pattern morphs under similar selective regimes elsewhere.