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Cryptosporidium spp. and Enterocytozoon bieneusi are common and important enteric parasites that can infect humans and animals, causing diarrhoea and systemic diseases. The objectives of the present study were to examine the prevalence and genetic variations of Cryptosporidium and E. bieneusi in pigs transferred from northeastern China to Ningbo city in Zhejiang Province. Cryptosporidium spp. was detected in 0.9% (2/216) of these samples and belonged to the zoonotic species Cryptosporidium parvum. A high E. bieneusi infection rate (25.0%, 54/216) was observed in this study, with 7 possible novel ITS genotypes (JLNB-1 to JLNB-7) and 10 known genotypes (EbpA, CM11, H, CM6, pigEBITS1, EbpC, CS-4, pigEBITS5, CHS5, and Henan-Ⅳ) identified, and zoonotic EbpA was the dominant genotype. Genotypes H and pigEBITS1 were reported for the first time in pigs in China. Phylogenetic analysis indicated that all the genotypes found in these samples belonged to zoonotic group 1. These findings indicated the potential threat of Cryptosporidium and E. bieneusi to humans or the environment during cross-regional transportation. An effective management control system should be built to avoid parasitic transmission as well as other animal diseases while travelling across different regions. In further studies, attention should be given to the transmission routes and the role of pigs as a potential source of human Cryptosporidium and E. bieneusi infections in China. • A high E. bieneusi infection rate with 7 possible novel ITS genotypes and 10 known genotypes belonged to zoonotic group 1. • Cryptosporidium parvum was identified in pigs. • Parasitic transmission during animals transportation across regions. [ABSTRACT FROM AUTHOR]