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<i>Enterocytozoon bieneusi</i> and <i>Encephalitozoon</i> spp. are microsporidian pathogens with zoonotic potential that pose significant public health concerns. To ascertain the occurrence and genotypes of <i>E. bieneusi</i> and <i>Encephalitozoon</i> spp., we used nested PCR to amplify the internal transcribed spacer (ITS) gene and DNA sequencing to analyze 198 fecal samples from red pandas from 6 zoos in China. The total rate of microsporidial infection was 15.7% (31/198), with 12.1% (24/198), 1.0% (2/198), 2.0% (4/198) and 1.0% (2/198) for infection rate of <i>E. bieneusi</i>, <i>Encephalitozoon cuniculi</i>, <i>Encephalitozoon intestinalis</i> and <i>Encephalitozoon hellem</i>, respectively. One red panda was detected positive for a mixed infection (<i>E. bieneusi</i> and <i>E. intestinalis</i>). Red pandas living in semi-free conditions are more likely to be infected with microsporidia (χ² = 6.212, df = 1, <i>p</i> < 0.05). Three known (SC02, D, and PL2) and one novel (SCR1) genotypes of <i>E. bieneusi</i> were found. Three genotypes of <i>E. bieneusi</i> (SC02, D, SCR1) were grouped into group 1 with public health importance, while genotype PL2 formed a separate clade associated with group 2. These findings suggest that red pandas may serve as a host reservoir for zoonotic microsporidia, potentially allowing transmission from red pandas to humans and other animals.