The pampas deer (Ozotoceros bezoarticus) is one of the most endangered neotropical mammals in Uruguay. Although it has a wide geographic distribution in south-eastern South America (from 5°S to 41°S), the habitat required by this species has been greatly reduced by agriculture and urbanisation. The species decline was due to human activities, and currently two isolated populations survive. The parasitological load is a good indicator of the health of the species and the ecosystem. The objective of the present study was to survey and determine the parasitological composition of the two Uruguayan pampas deer populations. We quantified the coproparasite load, by analysing the effect of seasonality through the year, the micro-ecosystem environment, the topography and also the livestock of the paddock. The taxonomic assessment was based on adult individuals obtained from the post mortem necropsy examination in individuals found dead in the field. The genera of the endoparasites recorded through the morphological eggs, larvae and/or adults were Trichuris, Capillaria, Strongyloides, Fasciola, Paramphistomum, Moniezia, Haemonchus, Ostertagia, Trichostrongylus, Oesophagostomum and Coccidias ooquiste. Our results showed that the parasitological community in the pampas deer is strongly correlated with the environmental conditions, topology, micro-ecosystem and the land use, as well as the effect of the livestock load. Moreover, because we have diagnosed the same genera of helminths in domestic ruminants, we recommend balancing the carrying capacities of the field paddocks, and performing periodical surveys of the livestock parasite load that will be helpful in maintaining control at lower values.