Objective To understand the prevalence of Cryptosporidium infection in diarrhea infants under 2 years old in Wuhan City,so as to provide the epidemiological evidence for the prevention and treatment of cryptosporidiosis. Methods The fecal samples from infants under 2 years old with diarrhea were collected in Hubei General Hospital and Central South Hospital in Wuhan City,Hubei Province from August 2014 to July 2015. The fecal samples were stored in 2.5%potassium dichromate at 4℃after filtered. The DNA was extracted from the fecal pellets with the phenol-chloroform method. The Cryptosporidium species were detected by a nested PCR assay targeting the SSU rRNA gene of the parasite. All the positive PCR products were sequenced on ABI 3100 automated sequencer,and the amplified sequences were compared to homologous sequences in the NCBI database by using the Basic Local Alignment Search Tool(BLAST). Phylogenetic analyses were performed by using the software MEGA (version 4.0)based on the Neighbour-Joining method. Results The human stool specimens(n=298)were screened for the presence of Cryptosporidium by nested PCR. The infection rate of Cryptosporidium was 3.02%(9/298). The infection rate of Cryp-tosporidium was 5.93%(7/118)in the infants between 1-2 years old,and the infection rate was 1.11%(2/180)in the infants un-der 1 year old,and there was a significant difference between the two groups(χ2 =4.13,P<0.05). The nine samples which were positive by nested PCR were successfully sequenced and compared with the reference sequences in GenBank. The results revealed the nine positive specimens were all infected with C. parvum,and two of them were co-infected with C. hominis. Neigh-bor-joining trees were constructed from the aligned partial SSU rRNA sequences of these nine isolates,and in the SSU rRNA lo-cus,the nine isolates were grouped with C. parvum. Conclusion There exists Cryptosporidium infection in the infants under 2 years old with diarrhea in Wuhan City,and the main species of Cryptosporidium is C. parvum.