Background: Noninvasive collection of feces is a cost-effective strategy for monitoring free-living wild mammals. The aim of this study was to search for carnivore and artiodactyl species and investigate the gastrointestinal parasites in their feces, in Itatiaia National Park, Brazil.

Methodology/Main Findings: Between 2017 and 2018, feces from carnivores and artiodactyls were collected along trails in the park. Host species were identified from these feces through macroscopic and trichological examination and through molecular biology using mitochondrial gene fragments. To investigate parasites, the Faust, Lutz and modified Ritchie and Sheather techniques and enzyme immunoassays were used to detect Cryptosporidium sp. antigens. A total of 244 stools were collected in three regions of the park. The species identified were C. brachyurus (39.7%), L. guttulus (21.3%), C. familiaris (5.3%), C. thous (0.8%), Puma yagouaroundi (0.8%), L. pardalis (0.4%), P. concolor (0.4%) and S. scrofa (4.9%). The overall positivity for parasites was 81.1%. Helminths were more frequently detected in carnivore feces (70.9%), especially eggs of the family Ascarididae and Toxocara sp. Protozoa presented higher frequency in artiodactyl feces (87.1%), especially coproantigens of Cryptosporidium sp. This zoonotic protozoon was detected in eight mammal species, including one that may be invasive: animals from crossbreeding of domestic pig with wild boar. High values for parasite structural richness (R’), Shannon (H’) and Simpson (D) parasite diversity indices were observed, especially in the feces of C. brachyurus (R’ = 12, H' = 2.2761, D = 0.887). Significant differences in parasite diversity were observed between C. brachyurus and C. familiaris; and between C. brachyurus and S. scrofa (pooled t test = 0.01 and 0.03, respectively). The highest values for parasite similarity (Sorensen test ≥ 0.8) were found among species that are taxonomically close, such as C. brachyurus and L. guttulus.

Conclusions/Significance: This was the first parasitological survey on carnivore and artiodactyl feces collected noninvasively in Brazil. It enabled animal identification through correlations using three techniques and diagnosis of highly frequent parasite structures that can infect these animals.