Taxonomy based on evolutionary relationships plays a critical role in science and society, as properly named units of biological diversity allows for immediate recognition of the general appearance and basic natural history of a particular lineage. Consequently, it could be argued that systematics, a field that investigates not only the classification of organisms but also their diversity and origins, is among the most important with relevance to all other disciplines within biology. The challenge is documenting species in nature; these units are there to find but doing so requires compiling a variety of different sources of data and methods to test hypotheses about diversity. Through this dissertation, I combine my background in classical taxonomy, natural history, and descriptive morphology with modern molecular phylogenetics, implementing Bayesian, Likelihood, and Parsimony optimality criteria, to stabilize taxonomy, detect cryptic diversity, and understand snake phylogeny. In particular, I incorporate important guidelines recently defined for integrative taxonomy, that assure accurate classification of biodiversity; these guidelines should become the new standard for all systematic revisions. To assess these guidelines, I have focused on a group and region where taxonomic and systematic knowledge is still very limited. Central and South American snakes are not only a point of continued systematic confusion but also understanding the evolutionary histories of venomous species may provide applications to medical treatment and human health. Using these methods of modern systematics I investigate two lineages of Neotropical snakes whose systematic history begins with classical Linnean taxonomy and progresses over the centuries with the advancement of systematic techniques. Cryptic lineages, in combination with inadequate sampling, obscure the complete diversity of this group. This dissertation incorporates several important sub-sections of systematics including an integrative systematic revision (chapter 2), detection of cryptic species (chapter 3), and placement of an enigmatic lineage within the tree of life (chapter 4). Overall, this research highlights how these guidelines for integrative taxonomy are paramount to achieving an informative and stable classification system. Systematic studies like this are becoming increasingly important in our current age of rapid biodiversity loss.