ABSTRACT Cryptosporidium species are the causative agent of cryptosporidiosis and common intracellular parasites that can infect a wide range of vertebrates, including snakes. In previous studies, Cryptosporidium species infections have been reported in snakes in Asia, Europe, and North America. However, limited information is available about the prevalence and molecular characterization of Cryptosporidium in captive snakes in China. Fecal specimens from 609 captive snakes were collected from Beijing (n = 227), Chengdu (n = 12), Dazhou (n = 359), and Ziyang (n = 11). The partial small-subunit ( SSU ) rRNA gene was amplified by nested polymerase chain reaction to determine the prevalence of Cryptosporidium , and a phylogenetic tree was constructed to assess evolutionary relationships and genetic characteristics. The overall prevalence of Cryptosporidium was 1.97% (12/609). BLAST and phylogenetic analysis of the small subunit ribosomal RNA ( SSU rRNA ) gene showed that the parasites belonged to Cryptosporidium serpentis . To the best of our knowledge, this is the first study to report the prevalence of Cryptosporidium in snakes of southwestern and northern China and provides preliminary data for the control and prevention of cryptosporidiosis in the investigated areas.