Pathoecology studies the environmental and cultural factors that contribute to the maintenance of infections or diseases in populations. Concerning parasites, it requires the evaluation of these factors based on the presence and life cycle of these organisms. For this reason, it is possible to apply this concept in the context of ancient populations in order to understand the parasite–host dynamic or even the health consequences faced by the members of the populations. This study aimed to apply the pathoecology concept in Pedra do Tubarão and Cemitério do Caboclo archaeological sites. Six coprolite samples were analyzed and 1 was positive for Spirometra sp. eggs. Spirometra is a cestode that has copepods as the first intermediate host; amphibians, reptiles, birds, and mammals as the second intermediate hosts; and felines and canines as definitive hosts. Humans can be infected by ingesting the first or second intermediate hosts and can develop sparganosis, which can cause health consequences depending on the location of the spargana. The presence of this parasite, of a water fount near the site, where the first intermediate host can live, and the findings of the bones of some of the second intermediate hosts in these sites, suggesting dietary purposes, indicate that this infection was probably present in this population.