Cryptosporidiosis is a zoonotic disease caused by the protozoan parasite Cryptosporidium. A total of 436 horse fecal samples were collected from 19 farms, and acid-fast staining method was used for primary screening. Cryptosporidium oocysts were found in 161 samples, among which 33 positive sample were selected for nested PCR, restriction fragment length polymorphism analysis and DNA sequencing of 18 S rDNA, showing 31 samples to be bovine C. parvum and 2 C. felis. The methods employed in this study should be useful as tools to identify cryptosporidiosis genotypes and species of livestock.