Abstract: In order to investigate species or genotype of the Cryptosoridia isolates that derived from different hosts in Henan province, the author amplified the complete sequences of the small-subunit rRNA ( 18S rRNA) gene and the 70 ku heat shock protein (HSP70) gene. Phylogentic analyses were performed using PAUP 4.0 and TREEPUZZLE 4.1.Species and genotypes of all Cryptosporidium isolates that derived from livestock, poultry and human in Henan were determined for understanding the mechanism of Cryptosporidium molecular epidemiology. We characterized the 18S rRNA and HSP70 genes of the isolates. Results of the phylogenetic analysis revealed that the Cryptosporidia human strain is Cryptosporidium parvum mouse genotype; the Cryptosporidia deer (wapiti) strain is C. parvum deer genotype, the two Cryptosporidia swine strains both are C. suis; the two Cryptosoridia quail strains belong to different species, one is C. bailey, the other is C．meleagridis; both the other Cryptosporidia birds strains (isolated from chicken and ostrich) are C. baileyi; the Cryptospridia isolates from cattle is C. andersoni.