Abstract: In order to investigate the pollution status of Cryptosporidium and Giardia in the Yangtze River Basin， 34 water samples were collected from 17 sampling points in 7 provinces and cities along the Yangtze River Basin in the flood season (July) and the dry season (November). Cryptosporidium oocysts and Giardia cysts were detected and counted under a microscope following a method involving concentration with precipitation， separation with density gradient and fluorescent staining. The results showed that the total detection rate of oocysts or cysts was 61.76%， while the detection rates of oocysts or cysts in the flood and dry season samples were 58.52% and 64.71%， respectively. From a regional perspective， the detection rate of Cryptosporidium in Sichuan Province was the lowest， i.e. 12.5%， while those in Hubei Province and Anhui Province were the highest， both with 75%. In addition， the detection rates of both Cryptosporidium and Giardia in Hubei Province were relatively high. The results of this study showed that all regions of the Yangtze River were polluted by Cryptosporidium and Giardia to varying degrees， and there were certain hidden dangers in water safety， especially when it used as a source of drinking water. It is necessary to strengthen the monitoring of water treatment removal efficiency to ensure the safety of drinking water for residents.