Pathways between genotype and phenotype, especially a behavioral phenotype, are complicated by many levels of biological organization, making direct connections difficult. An ideal model in behavioral genetics is the white-throated sparrow because a rearrangement of the second chromosome, which constitutes a supergene, is linked with territorial aggression. Birds with a copy of the supergene are more aggressive than those without it. The supergene has captured VIP, which encodes vasoactive intestinal peptide, a neuromodulator already known to be causal for aggression in other songbirds. VIP expression is higher in the anterior hypothalamus of birds with the supergene than in those without it and expression of VIP in this region predicts the level of territorial aggression regardless of genotype. Thus, VIP is a strong candidate to mediate this behavioral polymorphism. Here, we aimed to identify epigenetic mechanisms that could contribute to differential expression of VIP. We extracted and bisulfite-converted DNA from samples of hypothalamus in wild-caught adults and nestlings, and used high-throughput sequencing to measure DNA methylation of a region 1.2kb upstream of the VIP start site. We found that this region was less methylated in birds with the supergene than in those without it. In addition, methylation differed between the supergene allele and the standard allele at specific sites within this putative cis-regulatory element. This differential methylation provides a potential explanation for differential VIP expression in this species. This work represents an initial step toward understanding how differentiation of genetic sequence inside supergenes leads to the development of alternative behavioral phenotypes.