Color polymorphism and the genetic basis driving pattern variation in ectothermicsquamates is greatly under-studied outside of melanocytes. Variation in color and patternevolution in wild populations of squamates is a highly informative feature that reflectsdetails about defense strategies, feeding habits, environmental factors such as temperature,as well as overall fitness. Vipera berus is the most widely distributed and northernmostterrestrial snake in the world, yet they show very little variation in morphology across theirrange. In this study, we investigated the genetic basis of a rare phenotype not observed tothis degree in the entire range of V. berus using a combination of whole-genome shotgunsequencing, pairwise FST estimates, genome-scanning and a genome-wide association basedon 3,530,627 SNPs and 154 haplotypes. Seventeen populations of Vipera berus, as well asfive outgroup Vipera species, were sampled within twelve countries across Eurasia toanalyze the population structure of European vipers. Using these methods, we discovered15 candidate regions, five candidate genes, four potential candidate genes and six SNPssignificantly associated with the striped pattern in the isolated island population of Gossa.The most notable of these was the discovery of PMEL, a well known key component ofmelanosome pigmentation. Additionally, we compared two subspecies of Vipera berus toinvestigate why the nominate subspecies had greater success in colonizing their vast range.This resulted in the discovery of 24 candidate regions, five candidate genes and ninepotential candidate genes that significantly differentiated the two subspecies. Of these,SVMP was identified as a potential candidate gene, which has been suggested to improvedigestion efficiency of snakes in colder climates. Limitations of this experiment wereprimarily due to a lack of access to a thorough genome annotation for Vipera berus, whichprevented the identification of >70% of candidate regions and five significant SNPs usingthe genome annotation. Although these genes were not identified using the annotation, theybroaden the possibility of targeting these regions in the future and contribute to ourunderstanding of genetic variation as well as pigmentation genes among isolated wildpopulations of snakes. Our results provide insight into the parallel evolution and geneticbasis of pigmentation between ectothermic squamates using the unbiased approach ofgenome scanning, a method that has rarely been used in this context.