Background: Enterocytozoon bieneusi is a zoonotic pathogen with a wide range of animal host. In China, there are only a few reports of E. bieneusi infection in wild populations of Rhesus macaque. Here, we determined the prevalence of E. bieneusi in 9 populations of Rhesus macaque and assessed their zoonotic potential.Methods: A total of 324 fecal samples of Rhesus macaque were collected from 9 populations in 5 provinces (Sichuan, Chongqing, Qinghai, Tibet and Hainan) in China, and performed genotype of ITS gene to analyze the zoonotic potential.Results: 38 of the 324 (11.72%) specimens from wild Rhesus macaques were infected with E. bieneusi. 11 genotypes were identified including 3 known genotypes: D (n= 24), EbpC (n= 4) and SCC-2 (n= 1); 8 novel genotypes named Mul6 (n= 1), Mul7 (n= 1), Mul8 (n= 1), Mul9 (n= 1), Mul10 (n= 2), Mul11 (n= 1), Mul12 (n= 1) and Mul13 (n= 1). According to the phylogenetic analysis, Mul6, Mul7, Mul8, Mul9, Mul11 Mul12 and Mul13 were clustered into Group 1, while Mul10 were clustered into Group 5.Conclusions: To the best of our knowledge, this is the first study reporting the prevalence and genotypes of E. bieneusi in several wild populations of Rhesus macaque in China. It is concluded that, population of Rhesus Macaques is likely to prone of E. bieneusi transmission in many regions of China, which found the zoonotic genotypes D and EbpC and the novel genotypes with zoonotic potential, it should be paid more attention to prevent.