Coprolite science, human parasitism and ancient DNA methodology, converge most appropriately in the sub-specialty of archaeoparasitology – the study of prehistoric parasitism. In this study, we have applied targeted PCR to an archaeological sample from La Cueva de los Muertos Chiquitos, El Zape, Durango, Mexico, ~ AD 600. The addition of molecular analysis, resulted in the identification of a rare human parasite, previously unidentified, and a clarification of ambiguous morphological parasite remains. Discovery of an unexpected parasite has implications for the interpretation of human health in this prehistoric site. An additional analysis of previously generated Whole Genome Shotgun (WGS) Next-Generation Sequencing (NGS) data, resulted in the development of a series of filters to increase certainty of taxonomic identifications. The results of the NGS data manipulation failed to identify parasites in the dataset, but provides a foundation for a discussion of future research and current deficiencies in the reference databases. It is recommended that a combined morphological and molecular approach is the most robust methodology for archaeoparasitological research. It is also recommended that resources be routed into the development of NGS targeted approaches. A final recommendation that increased systematic effort be applied to adding parasite reference sequences to publicly available reference databases. Given that human parasitism impacts one third of the world population, any technology that increases the information retrieved, while creating a cost effective and robust methodology, will benefit both modern clinical researchers and prehistoric researchers. Therefore, work from prehistoric studies is directly applicable to the issue of parasitism in the modern world.