Species of Blastocystis Alexieff, 1911 are anaerobic intestinal protists found in humans and many kinds of animals that mainly cause diarrhea, abdominal pain and other clinical symptoms. At present, data on the prevalence and subtype diversity of species of Blastocystis in domestic rabbits are very limited. The purpose of this study was to characterise the infection rate and gene subtype distribution of Blastocystis sp. in domestic rabbits in Henan Province, Central China, and provide foundation for prevention and control of the disease caused by Blastocystis sp. in domestic rabbits. DNA was extracted from 286 fresh rabbit faecal samples collected from four areas of Henan Province, Central China. All DNA samples were screened using PCR and positive samples were sequenced to identify individual subtypes based on the small ribosomal subunit (SSU rRNA) gene. The overall infection rate of Blastocystis sp. in domestic rabbits in Henan Province was 15% (43/286). Three subtypes were identified, including ST1 (26/43, 60%), ST3 (5/43, 12%) and ST7 (12/43, 28%), all of which belonged to potentially zoonotic subtypes, ST1 was the dominant gene subtype. These results showed that infection with Blastocystis sp. was common in domestic rabbits in Henan Province, Central China, and was represented by zoonotic subtypes. Therefore, special attention should be paid to reduce the risk of transmission of Blastocystis sp. from domestic rabbits to humans.