Cryptosporidium spp. is a protozoan parasite of many vertebrates worldwide including avian hosts, causing gastroenteritis and diarrhea. Studies have been conducted on Cryptosporidium spp. in some avians, however, there is no information on Cryptosporidium spp. in pigeons from Anhui Province, China. To investigate the prevalence and assess the transmission burden of Cryptosporidium species in domestic pigeons, a total of 376 fecal samples were collected. The acid-fast staining and nested PCR amplification methods reveal a Cryptosporidium prevalence rate of 5.05% (19/376) and 1.86% (7/376), respectively. Furthermore, molecular characterization was identified as Cryptosporidium meleagridis. As this study is the first report on Cryptosporidium spp. in domestic pigeons in Anhui Province, we expect it to provide baseline information for further studies.