Significance The jararaca lancehead genome provides a comprehensive road map of the genomic context of pitviper toxin genes. Comparisons of these genomic segments across the phylogeny revealed an unexpectedly high number of toxin families that originated via the direct co-option of preexisting nontoxin genes, indicating that the snake toxin arsenal was mostly assembled from local elements of the ancestral genome. These results support a new perspective in venom evolution in which gene duplications in most toxin families occurred after, rather than before, initial toxin recruitment from nontoxin genes, contributing to the evolutionary optimization of snake venoms. They also emphasize the importance of correctly identifying orthologous loci to accurately trace the genomic pathways that lead to the evolutionary origination of new traits.