Selection is predicted to drive diversification within species and lead to local adaptation, but understanding the mechanistic details underlying this process and thus the genetic basis of adaptive evolution requires the mapping of genotype to phenotype. Venom is complex and involves many genes, but the specialization of the venom gland toward toxin production allows specific transcripts to be correlated with specific toxic proteins, establishing a direct link from genotype to phenotype. To determine the extent of expression variation and identify the processes driving patterns of phenotypic diversity, we constructed genotype-phenotype maps and compared range-wide toxin-protein expression variation for two species of snake with nearly identical ranges: the eastern diamondback rattlesnake (Crotalus adamanteus) and the eastern coral snake (Micrurus fulvius). We detected significant expression variation in C. adamanteus, identified the specific loci associated with population differentiation, and found that loci expressed at all levels contributed to this divergence. Contrary to expectations, we found no expression variation in M. fulvius, suggesting that M. fulvius populations are not locally adapted. Our results not only linked expression variation at specific loci to divergence in a polygenic, complex trait but also have extensive conservation and biomedical implications. C. adamanteus is currently a candidate for federal listing under the Endangered Species Act, and the loss of any major population would result in the irrevocable loss of a unique venom phenotype. The lack of variation in M. fulvius has significant biomedical application because our data will assist in the development of effective antivenom for this species. N ATURAL selection can be a powerful force driving rapid diversification within species and is predicted to lead to local adaptation through the increase in frequency of mutations in gene-regulatory or protein-coding regions (Stern 2000;Hoekstra and Coyne 2007;Carroll 2008;Muller 2007). Expression variation at single loci has produced adaptive phenotypic divergence in the beaks of Darwin's finches (Abzhanov et al. 2004), coat color in mice (Manceau et al. 2011), and mimicry in butterflies (Reed et al. 2011). Most traits, however, are products of poorly characterized developmental pathways involving many loci. Many of the fundamental features of evolving systems, such as evolvability, epistasis, pleiotropy, and basic variational properties (Rokyta et al. 2008(Rokyta et al. , 2009(Rokyta et al. , 2011bWager 2008;Chou et al. 2011;Woods et al. 2011;Hill and Zhang 2012), result from the relationship between genotype and phenotype (Stadler et al. 2001;Hansen 2006), but the ability to study this relationship directly in polygenic traits is rare. Therefore, linking gene-regulatory changes to adaptive evolution in polygenic, complex phenotypes remains a challenge (Romero et al. 2012;Savolainen et al. 2013).Snake venoms are complex cocktails of 40-100 proteinaceous toxins (Boldrini-França et ...