Background: Blastocystis is a commonly identified intestinal protozoan in humans and various animals. Few studies are available regarding the genetic characterization of Blastocystis infections in pigs in China. Methods: In this study, 801 fecal samples were collected from seven large-scale pig farms in Xinjiang and tested by polymerase chain reaction. Results: The average infection rate of Blastocystis was 21.7% (174/801); the infection rates for pre-weaning piglets, post-weaning piglets, fattening pigs, and sows were 7.1%, 10.0%, 31.8%, and 41.9%, respectively (χ 2 = 104.89; P < 0.01). Blastocystis subtypes ST1 ( n = 7), ST3 ( n = 2), and ST5 ( n = 165) were identified using sequence analysis of the small-subunit ribosomal RNA gene, with subtype ST5 being predominant in each of the pig farms. All the age groups were positive for Blastocystis . ST3 and ST5 were identified in pre-weaning piglets, and ST1, ST3, and ST5 in post-weaning piglets. In contrast, only the ST5 subtype was observed in fattening pigs and sows. Genetic polymorphisms were observed at the intra-subtype level, including two variations for ST1 (ST1A, ST1B), and seven for ST5 (ST5A to ST5G), by sequence alignment analysis and phylogenetic analysis. Conclusions: A high prevalence of Blastocystis was detected in pigs in Xinjiang, China. The infection rate increased significantly with increasing age of the pigs. ST5 was the predominant Blastocystis subtype in all age groups. Subtypes ST1, ST3, and ST5 may emerge as zoonotic pathogens in some areas of China because of the large scale of the pork industry and close contact between pigs and humans. More studies are needed to elucidate the transmission and public health significance of Blastocystis in pigs in various areas. Key words: Blastocystis , SSU rRNA, genetic polymorphism, pig, Xinjiang