The growing popularity of reptiles has contributed to their reproduction in captivity. When subjected to stressful environments, such as the presence of a higher number of humans and animals, reptiles may become more susceptible to parasites. Endoparasites in captive animals may cause several clinical signs ranging from mild to severe: lethargy, anorexia, diarrhea, cloacal/penile prolapse, infertility, intestinal malabsorption syndrome, and weight loss, among others. This study aimed to assess the presence of gastrointestinal parasites in fecal samples of reptiles from a Portuguese zoo through two techniques: a fecal flotation test (using a saturated sodium chloride solution) and Mini-FLOTAC. Ninety-nine samples belonging to 22 different animal species were collected and analyzed. Parasites were identified in 53.5% of the samples. Chelonians had a higher frequency (100%), followed by lizards (56.8%) and snakes (47.4%). The eggs/oocysts found were oxyurids (36.4%), strongylids/Kalicephalus sp. (8.1%), Eimeria sp. (5.1%), Hymenolepis spp. (5.1%), ascarids (4.0%), and Isospora sp. (2.0%). Both techniques presented the same results for each sample. The high prevalence of oxyurids, as well as of other parasites, can be explained by possible environmental contamination as these reptiles are kept in captivity. This study indicated the importance of assessing parasitic infections in reptiles in zoos, where routine coprological examinations should always be considered, as well as adequate prophylaxis.