Entamoeba species are common intestinal parasites in primates. The Tibetan macaque (Macaca thibetana) is an endemic species in China, and the habitat of the wild population in Mount Gongga has the highest altitude. In this study, we collected 84 fecal samples from wild Tibetan macaques in Mount Gongga. PCR amplifications of SSU rRNA genes were used to detect seven Entamoeba species, and the differences in seasonal prevalence were further analyzed. Additionally, we genotyped the potentially pathogenic E. nuttalli based on the tRNA-linked short tandem repeat (STR) loci and further analyzed the phylogenetic relationship among the genotypes obtained from Tibetan macaques and other primates. The results indicate a high prevalence of Entamoeba spp. (88.1%, 74/84), and four species were identified: E. chattoni (86.90%), E. coli (60.71%), E. hartmanni (48.81%), and E. nuttalli (73.81%), meanwhile, there are common mixed infections (67/74, 79.76%). The prevalence of four Entamoeba species was all lower in spring and higher in winter. In addition, phylogenetic analysis revealed a potential new subtype (ST4) of E. hartmanni in wild Tibetan macaques. Based on tRNA-STR loci, there was a high genotype diversity and genetic differentiation of E. nuttalli: 14 genotypes of E. nuttalli were obtained, and the phylogenetic tree showed the genotypes obtained in this study were distinct from that found in Myanmar and Nepal. Present results indicate the general prevalence of potentially pathogenic E. nuttalli in Tibetan macaques, which suggests we should pay attention to the risk of zoonotic transmission of these Entamoeba species.