cTo explore the genetic diversity, host specificity, and zoonotic potential of Enterocytozoon bieneusi, feces from 348 stray and pet dogs and 96 pet cats from different locations in China were examined by internal transcribed spacer (ITS)-based PCR. E. bieneusi was detected in 15.5% of the dogs, including 20.5% of stray dogs and 11.7% of pet dogs, and in 11.5% of the pet cats. Higher infection rates were recorded in the >2-year and the 1-to 2-year age groups in dogs and cats, respectively. Altogether, 24 genotypes, including 11 known and 13 new, were detected in 65 infected animals. In 54 positive dogs, 18 genotypes, 9 known (PtEbIX, O, D, CM1, EbpA, Peru8, type IV, EbpC, and PigEBITS5) and 9 new (CD1 to CD9), were found. In contrast, 8 genotypes, 4 known (D, BEB6, I, and PtEbIX) and 4 new (CC1 to CC4), were identified in 11 infected cats. The dominant genotype in dogs was PtEbIX (26/54). Phylogenetic analysis revealed that 8 known genotypes (D, Peru8, type IV, CM1, EbpC, PigEBITS5, O, and EbpA) and 7 new genotypes (CD1 to CD4 and CC2 to CC4) were the members of zoonotic group 1, whereas genotypes CD7, CD8, and CD9 together with PtEbIX belonged to the dog-specific group, and genotypes CD6 and CC1 were placed in group 2 with BEB6 and I. Conversely, genotype CD5 clustered with CM4 without belonging to any previous groups. We conclude that zoonotic genotypes are common in dogs and cats, as are host-specific genotypes in dogs. M icrosporidia, obligate eukaryotic intracellular pathogens, are considered to be highly diverged and specialized parasites, formerly classified as protozoa (1) and recently included in the fungus kingdom without further subdivision (2). They infect a wide variety of vertebrate and invertebrate hosts (3). Among the human-infecting microsporidian species, Enterocytozoon bieneusi is the most frequently diagnosed in AIDS patients with chronic diarrhea, organ transplant recipients, children, the elderly, and patients with malignant diseases and diabetes (4, 5). In addition, E. bieneusi has been reported in various wild, domestic, and companion mammals and birds worldwide (4, 6). Thus, microsporidiosis by E. bieneusi is regarded as a zoonosis, although the range of animal hosts and their involvement in transmission are poorly understood.Recent molecular approaches based on sequence and phylogenetic analyses of the internal transcribed spacer (ITS) of ribosomal DNA (rDNA) enable us to assess the host specificity and public health significance of the organism (6, 7). There are now at least 204 reported ITS genotypes of E. bieneusi, and new genotypes have been identified in various animals, humans, and water bodies (6,(8)(9)(10). In phylogenetic analysis, these genotypes form some unique groups. Group 1 is found in humans and animals, while groups 2 to 8 are found mostly in specific hosts and wastewater (7,8,11).Recently, zoonotic E. bieneusi genotypes have been reported in AIDS patients, children, nonhuman primates, pigs, and urban wastewater in China (8,[10][11][12][13][14][15][16]. However, studies...