As a result of conflict with livestock in the early 20th century, the population of the rarest wolf subspecies, the Mexican wolf (Canis lupus baileyi) was reduced to only five individuals by 1980. The Mexican Wolf Recovery Program (MWRP) was formed to re-establish Mexican wolves in the native range. The management plan acknowledges the negative effects disease can have on threatened populations. Wolves share the re-introduction landscape with dogs, coyotes, foxes, and other mammals that can be infected by the same pathogens. So far, the managed population of Mexican wolves (captive and free-ranging animals) has not experienced a severe threat of disease and is actively being monitored for several viral and bacterial pathogens. However, the management strategy acknowledges that the presence of disease would likely reflect disease dynamics in other canine species, like coyotes, with higher abundances in that landscape. We know that wild canines can have intestinal parasites that can harm the host and also be transmitted to domestic animals and humans: Many of the roundworms and tapeworms that infect pets also occur in coyotes. Hydatid cysts caused by Echinococcus granulosus can occur in humans and livestock. The protozoan Neospora, which uses canines and ungulates in its life-cycle, causes abortions in livestock. Given some of these negative effects, it is important that we gather baseline data on parasites. In this study, I aim to fill in some of the gap in monitoring of intestinal parasites in this population by examining scat samples from coyotes and wolves. I use traditional methods in parasitology and next-generation sequencing of the universal eukaryotic primer for 18S sRNA and associated analysis techniques, such as QIIME.