Enterocytozoon bieneusi was detected in 128 (15.26%) of 839 fecal specimens from 23 nonhuman primates species in China based on 16S rRNA locus.At ITS marker,126 specimens were successfully amplified,belonging to genotypes Type Ⅳ,D,Peru8,Henan Ⅴ,Perul 1,PigEBITS7 and 3 novel ones (CM1,CM2,CM3).MLST employing four micro and minisatellites (MS 1,MS3,MS4,MS7) and ITS was used to analyze population genetics of 85 isolates successfully amplified at all five loci,which yielded 59 multilocus genotypes.Linkage disequilibrium (LD) was measured using both multilocus sequences and allelic profile data.The observation of strong and significant LD with limited recombination in multilocus sequence analysis indicated the presence of overall clonal population structure ofE.bieneusi,which was supported by allelic profile data analysis.Fu s selective neutrality test demonstrated the absence of neutral mutations and molecular selection.The population structure of common ITS genotypes (CM1,Type Ⅳ and D) was compared.Strong LD in multilocus sequence analysis versus insignificant LD and/or LE in allelic profile data analysis impliedepidemicpopulation in common ITS genotypes.No significant genetic isolation was evidenced by either phylogenetic or substructural analyses.The population genetics was also compared among the sub:population 1 (contained mainly genotype Type Ⅳ),sub:population 2 (contained mainly genotypes CM 1 and D),sub:population 3 (contained mixed genotypes) and sub:population 4 (contained genotype Henan Ⅴ).The presence of strong LD in multilocus data analysis with insignificant LD and/or LE in allele profile data analysis suggested the epidemic population in sub:populations.Enterocytozoon bieneusi,Multilocus sequence typing,Genetic diversity,Population genetics,Linkage disequilibrium,Population structure,Nonhuman primates.