Cryptosporidium spp. cause enteric diseases in a wide range of animals, including dairy cattle. However, limited information is available regarding prevalence and molecular characterization of Cryptosporidium spp. in dairy cattle in Gansu province and Ningxia Hui Autonomous Region (NXHAR), northwest China. A total of 2945 dairy feces samples (1257 from Gansu province and 1688 from NXHAR) were collected between December 2012 and March 2014 and were tested by PCR amplification of the small subunit (SSU) rRNA gene. A total of 150 (5.09 %, 58 from Gansu and 92 from NXHAR) samples were PCR-positive for Cryptosporidium, and the prevalence is associated with the region and age of dairy cattle. Species identification showed Cryptosporidium andersoni in 36 samples (24.00 %, 19 from NXHAR and 17 from Gansu), Cryptosporidium ryanae in 24 samples (16.00 %, 13 from NXHAR and 11 from Gansu), Cryptosporidium bovis in 70 samples (46.67 %, 41 from NXHAR and 29 from Gansu), and Cryptosporidium parvum in 20 samples (13.33 %, 19 from NXHAR and 1 from Gansu). A DNA sequence analysis of the gp60 gene suggested that all the 20 C. parvum isolates represented subtype IIdA15G1. These findings indicated the presence of zoonotic Cryptosporidium in Gansu and NXHAR. This is the first report of four species of Cryptosporidium (C. andersoni, C. ryanae, C. bovis, and C. parvum) infection in dairy cattle in Gansu province. This is also the first report of C. ryanae infection in dairy cattle in NXHAR. Effective control strategies should be implemented to prevent and control Cryptosporidium infection in dairy cattle and humans.