Entamoeba is a genus of gastrointestinal protozoon that is transmitted through contaminated food and water. This protozoon is commonly found in human and nonhuman primates. Contact between humans and Formosan rock macaques (Macaca cyclopis) has become more frequent due to food provisioning; accordingly, concerns regarding zoonotic pathogen transmission through the fecal-oral route have increased. For example, surveillance of intestinal parasites in wild Formosan rock macaques indicated that Entamoeba infection was the most prevalent type of intestinal parasite infection. The morphologies of pathogenic and nonpathogenic species are difficult to distinguish. In this study, we collected fecal samples from wild Formosan rock macaques in the Shoushan National Nature Park (Kaohsiung, Taiwan) and adopted both morphologic and molecular methods for Entamoeba species identification. In total, we collected 208 fecal samples with a 57.7% (120/208, 95% confidence interval: 50.9–60.4%) prevalence of Entamoeba infection. Four Entamoeba species were identified: three nonpathogenic species, Entamoeba coli (19%), Entamoeba chattoni (50%), and Entamoeba hartmanni (11%), and one potentially pathogenic species, Entamoeba nuttalli (20%). Our study revealed the risk of zoonotic transmission of these Entamoeba species to humans. To address relevant public health and wildlife conservation concerns, further research is required to fully understand the virulence of E. nuttalli isolated from Formosan rock macaques.