A total of 124 fecal specimens were collected from four deer farms in Zhengzhou City, China and examined for Cryptosporidium by Sheather’s sugar flotation technique. Cryptosporidim oocysts were detected in two 1-year-old sika deer, and one of the two specimens was genotyped by sequence and phylogenetic analyses of the small subunit ribosomal RNA (rRNA) (18S rRNA), 70-kDa heat shock protein (HSP70), actin, and Cryptosporidium oocyst wall protein (COWP) genes. Results obtained suggested that the Cryptosporidium studied belonged to Cryptosporidium cervine genotype, although slight sequence differences were noticed at the three loci. The similarities between this isolate and other Cryptosporidium cervine genotype isolates were 99.1–99.8%, 9.8%, 99.7%, and 100% at the 18S rRNA, HSP70, actin, and COWP loci, respectively. This study is the first report of Cryptosporidium infection in sika deer in China.