The present study was conducted to investigate the prevalence and genotypes of Cryptosporidium in bats. A total of 247 bats, belonging to Rhinolophus sinicus, Rousettus leschenaultia, Aselliscus stoliczkanus, and Hipposideros fulvus, were collected in Yunnan Province, Southwestern China, and the intestinal tissues were examined for Cryptosporidium infection by PCR amplification of the small subunit ribosomal RNA (SSU rRNA). The overall infection rate was 7.7% (95% CI, 4.5 to 11.0%), with R. sinicus having the highest level at 9.5% (95% CI, 2.8 to 16.1%) followed by A. stoliczkanus at 7.8% (95% CI, 2.2 to 18.9%), H. fulvus at 7.2% (95% CI, 1.1 to 13.4%), and R. leschenaultia at 5.7% (95% CI, 1.2 to 15.7%). DNA sequence and phylogenetic analyses based on SSU rRNA revealed the presence of 2 novel genotypes, designated as Cryptosporidium bat genotype I in A. stoliczkanus and R. sinicus and Cryptosporidium bat genotype II in R. leschenaultia, R. sinicus, and H. fulvus. This is the first report of Cryptosporidium genotypes in bats. Further biological and genetic characterization is needed to determine the relationship of the 2 novel genotypes to established Cryptosporidium species–genotypes.