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Yunling cattle is an unique cattle breed distributed in Yunnan Province, southwestern China. It is yet to know whether Yunling cattle are infected with Giardia duodenalis and Cryptosporidium spp.. The objectives of the present study were to investigate the prevalence and characterize the assemblages of G. duodenalis and species of Cryptosporidium spp. in Yunling cattle in Yunnan province. The overall prevalence of G. duodenalis and Cryptosporidium spp. were 10.49% (41/391) and 0.77% (3/391), respectively. The age was considered as the risk factor for Yunling cattle infection with G. duodenalis (χ 2 = 8.082, OR = 2.56, P = 0.004). Two assemblages of G. duodenalis , assemblage A (n = 1) and assemblage E (n = 40), were identified by amplification of the β-giardin (bg) and glutamate dehydrogenase (gdh) gene loci using the nested PCR methods. Furthermore, Cryptosporidium andersoni (n = 1) and Cryptosporidium ryanae (n = 2) were detected by nested PCR targeting the small subunit (SSU) rRNA gene. This is the first report of G. duodenalis and Cryptosporidium spp. in Yunling cattle in China, which provided baseline date for further studies of the prevalence, genetic identity, and public health potential of these parasites in Yunling cattle. • This study investigated the prevalence and genotypes of G. duodenalis and Cryptosporidium spp. in Yunling cattle. • The prevalence of G. duodenalis and Cryptosporidium spp. were 10.49% and 0.77%, respectively. • Two assemblages of G. duodenalis and Cryptosporidium andersoni and Cryptosporidium ryanae were observed. • This is the first report of G. duodenalis and Cryptosporidium spp. in Yunling cattle in China. [ABSTRACT FROM AUTHOR]