This study investigated 319 fecal specimens of cats(n =52)and dogs(n =267)from Heilongjiang province,China for the prevalence and genetic characteristics of Cryptosporidium,Enterocytozoon bieneusi,and Giardia duodenalis.PCR and DNA sequence analysis of the small subunit rRNA gene identified C.felis and C.parvum in one cat each(3.8%)and C.canis and C.ubiquitum in 6 dogs(2.2%).Polymorphisms in the ribosomal internal transcribed spacer and phylogenetic analysis characterized zoonotic E.bieneusi genotypes D,EbpC,NED1,and NED2 and host-adapted ones NED3,NED4,and PtEb Ⅸ in 18 dogs(6.7%)and human-pathogenic genotypes D and Ⅳ in 3 cats(5.8%).Genotyping based on the hypermutation of G.duodenalis triosephosphate isomerase gene(TPI)facilitated identification of assemblage F in a cat(1.9%)and assemblages C and E in 12 dogs(4.5%).Subtypes of G.duodenalis isolates were determined by measuring the diversity of both TPI nucleotide and amino acidsequences.C.canis,C.felis,C.parvum,E.bieneusi genotypes D,EbpC,and Ⅳ,and G.duodenalis assemblage C identified herein have been documented in human infections in China.C.canis,C.parvum,C.ubiquitum,and E.bieneusi genotypes D,EbpC,and Ⅳ carried by cats or dogs also existed in wastewater in China.The finding suggested pet animals could be reservoirs for human cryptosporidiosis,microsporidiosis,and giardiasis and potential sources of water contamination in China.