To identify Cryptosporidium species/genotypes in sheep in China and to elucidate the endemic transmission of cryptosporidiosis, a total of 1,701 fecal samples from five farms in four prefectures in Henan Province (central China) were examined. Eighty-two Cryptosporidium-positive samples were analyzed by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis of the small subunit (SSU) rRNA gene and PCR analysis of the 60 kDa glycoprotein (gp60) gene, and 41 were further analyzed by DNA sequencing of the PCR products. The SSU rRNA-based PCR identified two Cryptosporidium species and one genotype, including the Cryptosporidium cervine genotype (74/82), Cryptosporidium andersoni (4/82), and Cryptosporidium xiaoi (4/82). The cervine genotype was found in all age groups, C. xiaoi in lambs, and C. andersoni in ewes. There were intragenetic differences in the SSU rRNA gene sequences of the Cryptosporidium cervine genotype and C. xiaoi. No Cryptosporidium parvum was detected by both SSU rRNA- and gp60-based PCR assays. These findings suggest that sheep are a potential source for zoonotic infections of the Cryptosporidium cervine genotype.