Blastocystis is a common intestinal protozoan in humans and various animals worldwide. A few studies have reported the genetic characterization of Blastocystis in pigs in China, but no epidemiological data are available from the Xinjiang Uygur Autonomous Region. In this study, 801 fecal samples were collected from seven scale pig farms in Xinjiang and tested by polymerase chain reaction and sequence analysis of the partial SSU rRNA gene. The average infection rate of Blastocystis was 21.7% (174/801), with 7.1% in preweaning piglets, 10.0% in postweaning piglets, 31.8% in fattening pigs, and 41.9% in sows (χ2 = 104.89; P < 0.01). Blastocystis subtypes ST1 (7/174), ST3 (2/174), and ST5 (165/174) were identified, with subtype ST5 being predominant in each of the pig farms and in each of the age groups. ST3 and ST5 were identified in preweaning piglets, and ST1, ST3, and ST5 were identified in postweaning piglets. In contrast, only the subtype ST5 was observed in fattening pigs and sows. Genetic polymorphisms were observed at the intrasubtype level, including two variations of ST1 (ST1A, ST1B), and seven of ST5 (ST5A to ST5G), by sequence alignment analysis and phylogenetic analysis. More studies are needed to elucidate the transmission and public health significance of Blastocystis in pigs in various areas. © 2020 International Society of Protistologists.