The The media animal that come from farms such as rodents and flies are widely distributed and high fecundity,they can be a reservoir for a variety of pathogens that can lead to the prevalence of a variety of Zoonosis,which including bacterial diseases,viral diseases and parasitic diseases.The disease spread by media animal do a serious threat to human and animal whose mode of transmission is complex and diverse,because of the high mortality or morbidity,to strengthen the spread of disease and host media animal etiology and molecular biology studies,will contribute to the prediction and control of the disease.In order to understand the infection of intestinal parasites in rodents come form farms,we examined 232 rodents samples (168 Rattus norvegicus 168,31Mus musculus,33Rattus tanezumi) from four farms in Henan province and Fujian province using issue pressure plate method,Lugols iodine staining,Sheathers sugar flotation technique and acid-fast-method.The results showed that a total of 11 kinds of intestinal parasites (Giardia,Cryptosporidium,coccidia,Hymenolepis nana Hymenolepis diminuta,Strongylida sp.,Syphacia sp.,Strongyloidia sp.,Trichuris sp.,Hookworm and Aspiculuris tetraptera) and two tissue parasites (Strobilocercus and Capillaria hepatica) .The total infection rate of R.norvegicus was the highest in three kinds of rodents,that was 82.1%; then,R.tanezumi 60.6%; last,Mus musculus,19.1%.In order to identify genotype or subtype of Giardia and Cryptosporidium isolates from farms in Henan Province and Fujian Province,all the microscopy-positive samples of Giardia were took to be amplified by nested PCR at three loci,Triosephosphate isomerase (TPI) ,glutamate dehydrogenase (GDH) and beta-giardin (bg) loci.Then,Blast tool was used to search homological sequences in NCBI,after that,homological sequences were alignmented.Phylogenetic tree and homological analysis were made by some biological softwares such as Clustal X 1.81 and DNAstar 4.0.The results showed that all the 14 samples were belonging to assemblage G.Then all the samples were took to be amplified by nested PCR at two loci,the small subunit rRNA (18S) and the 60-kDa glycoprotein (GP60) loci.Then,Blast tool was used to search homological sequences in NCBI,after that,homological sequences were aligned.Phylogenetic tree and homological analysis were made by some biological softwares such as Clustal X 1.81 and DNAstar 4.0.The results showed that 12 samples were Cryptosporidium.Parvum IIdA15G1,7 samples were Cryptosporidium muris.In order to identify genotype or subtype of Giardia and Cryptosporidium isolates carryied by flies from farms,800 flies be captured with sticky fly paper,form farms in Zhengzhou Henan province,which be equipartition to 40 groups.all the 40 groups were took to be amplified by nested PCR at five loci,Triosephosphate isomerase (TPI) ,glutamate dehydrogenase (GDH) ,beta-giardin (bg) ,the small subunit rRNA (18S) and the 60-kDa glycoprotein (GP60) loci.Then,Blast tool was used to search homological sequences in NCBI,after that,homological sequences were alignmented.Phylogenetic tree and homological analysis were made by some biological softwares such as Clustal X 1.81 and DNAstar 4.0.The results showed that all the 4 positive samples of Giardia were belonging to assemblage E5,and all the 4 positive samples of Cryptosporidium were C.Parvum IIdA19G1.The zoonosis genotypes of Giardia and Cryptosporidium was found in rodents and flies in this study,so it is of significance important significance of public health to research the giardiasis and Cryptosporidiosis of rodents and flies.Investigation of Giardiasis and Cryptosporidiosis and molecular characteristics of them in rodents and flies have not been reported in China.Therefore,The present study results will provide a reference for research the Giardia and Cryptosporidium of rodents and flies such as molecular epidemiology,biologic characters and the relationship of germ line evolution between the isolates.