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Simple Summary: We have conducted a 10-year coprological study of animals housed in two zoological institutions with different housing conditions to assess parasite biodiversity and prevalence, their relationship with host class (mammal/bird), diet (carnivorous/omnivorous/herbivorous), and enclosure characteristics (soil type, isolation from wild fauna), and evaluated the risk of transmission to humans. A total of 4476 faecal samples from 132 mammal species and 951 samples from 86 avian species were examined, with 62.1% of mammal species and 12.8% of avian species testing positive. Statistically significant differences were found based on diet type; few carnivorous species were detected infected, primarily by nematodes, while many herbivorous and omnivorous species were primarily infected by protists. No statistically significant differences were observed based on soil type (artificial, natural, mixed) and isolation level (isolated/accessible). Several parasite species found in the study (Entamoeba spp., Giardia spp., Balantioides coli, Trichuris spp.) could potentially be transmitted between housed animals, wild fauna, and humans. Regular analyses of the animals and implementation and follow-up of health programs would minimise transmission risks between housed animals, wild fauna, and humans. We have conducted a 10-year-long coprological study of the animals housed in two zoological institutions (ZooAquarium and Faunia, Madrid, Spain) to assess the parasite biodiversity, prevalence, and their relation with host class, diet, and enclosure type (soil type and level of isolation from wild fauna). A total of 4476 faecal samples from 132 mammal species and 951 samples from 86 avian species were examined. The results indicated that only 12.8% of avian species had parasites at least once during the study period, whereas 62.1% of mammal species tested positive. Predominantly, protists (Entamoeba, flagellates, and ciliates) and nematodes (mainly Trichuris) were identified in the findings. Carnivorous species were primarily infected by nematodes, while herbivorous and omnivorous species were mainly infected by protists. The number of infected herbivorous and omnivorous species was significantly greater than carnivorous species. Differences were observed based on soil type (artificial, natural, mixed) and isolation level (isolated/accessible), but these differences were not statistically significant. Several parasites (Entamoeba spp., Giardia spp., Balantidoides coli, Trichuris spp.) could potentially be transmitted between humans and some mammals and birds. Regular animal analyses and a personnel health program in the institutions would minimise transmission risks between zoo animals, wildlife, and humans. [ABSTRACT FROM AUTHOR]