Enterocytozoon bieneusi
is a zoonotic pathogen with worldwide distribution. Among the 11 established groups of
E. bieneusi
genotypes based on phylogenetic analysis of the ribosomal internal transcribed spacer (
ITS
), the human-infective potential and population genetics of the Group 1 genotypes from diverse hosts are well characterized. In contrast, Group 2 genotypes from ruminants have unclear population genetics, leading to poor understanding of their host range and zoonotic potential. In this study, we sequence-characterized 121 Group 2 isolates from dairy cattle, beef cattle, yaks, Tibetan sheep, golden takins, and deer from China at five genetic loci (
ITS
, MS1, MS3, MS4 and MS7), comparing with data from 113 Group 1 isolates from nonhuman primates. Except for MS7, most of the genetic loci produced efficient PCR amplification and high nucleotide identity between Groups 1 and 2 of
E. bieneusi
genotypes. In population genetic analyses of the sequence data, a strong linkage disequilibrium was observed among these genetic loci in the overall Group 2 population. The individual
ITS
genotypes (I, J and BEB4) within Group 2, however, had reduced linkage disequilibrium and increased genetic exchanges among isolates. There was only partial genetic differentiation between Group 1 and Group 2 genotypes, with some occurrence of genetic recombination between them. Genetic recombination was especially common between genotypes I and J within Group 2. The data presented indicate a high genetic identity between Group 1 and Group 2 genotypes of
E. bieneusi
, which could be responsible for the broad host range and high zoonotic potential of Group 2 genotypes in China. As there is no effective treatment against
E. bieneusi
, the One Health approach should be used in the control and prevention of zoonotic transmission of the pathogen.