Enterocytozoon bieneusi is a common opportunistic pathogen found in both humans and animals. As companion animals live in close contact with human being, they may act as a zoonotic reservoir and play an important role in transmitting this parasite to humans. We evaluated the prevalence, genotypic diversity and zoonotic potential of E. bieneusi in dogs and cats in eastern China during Apr to Dec 2013.Fecal specimens from 315 dogs and 143 cats from veterinary hospitals in eastern China were examined in 2015 by internal transcribed spacer (ITS)-based PCR.E. bieneusi was detected in 8.6% of canine and in 1.4% of feline samples. Seven genotypes of E. bieneusi were identified, including four known genotypes (PtEb IX, EbpC, Type IV and D) and three novel genotypes, named CHD1, CHD2 and CHD3. The dominant genotype in dogs was PtEbIX (59.3%; n=16/27). Five (CHD1, EbpC, CHD2, D and Type IV) of the seven genotypes were in the so-called zoonotic group 1, whereas genotypes PtEbIX belonged to the dog-specific group and genotypes CHD3 were placed in group 2.Dogs are predominately infected with host-specific genotypes of E. bieneusi, and the finding of several zoonotic genotypes in dogs and cats reminds us of potentially zoonotic transmission of microsporidiosis.