South American camelids (SAC) played a central biocultural role in Andean communities until today. Paleoparasitology, a discipline examining parasite remains from ancient times, can shed light on SAC, animals closely related to humans, providing insights into camelid populations, societies and the environment in the past. The objectives of this study are (1) to provide new insight into the parasite diversity of SAC from the Southern Puna, (2) to compare parasite diversity between different sites, and (3) to interpret the findings in relation to environmental and cultural changes in the Puna over time. The coprolites studied proceed from three archaeological sites in the Southern Puna: Cueva Inca Viejo (CIV), Punta de la Peña 4 (PP4) and Piedra Horadada 2 (PH2). A total of 153 coprolites were studied, subjected to rehydration, homogenization, filtration and spontaneous sedimentation. The assignation of the zoological origin of coprolites as SAC was based on their morphology, biogeographic origin, the presence of Eimeria macusaniensis and Lamanema chavezi/Nematodirus lamae and aDNA analysis. Seventeen parasite taxa belonging to Apicomplexa, Nematoda and Platyhelminthes were found, representing the highest richness recorded in ancient times until now. A noteworthy finding was the recovery of zoonotic species like Fasciola hepatica and capillariids, providing insight into possible zoonotic infections in ancient Andean populations. The record of Moniezia sp. and Strongyloides sp. suggest their presence in native Andean species before the arrival of Hispanic societies. The results revealed a parasitic fauna consistent with both modern and paleoparasitological studies. Variations in the composition of parasite assemblages were observed over time and between sites.