Background: Blastocystis, a highly prevalent eukaryotic parasite, has been identified in a wide range of hosts, including humans, domestic and wild animals. Many animals are potential sources of Blastocystis infection for humans, while few information about the prevalence of Blastocystis in wild animals have being documented. Therefore, the present study was designed to investigate the prevalence and subtypes of Blastocystis in wild animals of Sichuan Wolong National Natural Reserve, southwestern of China, so as to assess the zoonotic potential of these animals.Methods: A total of 300 faecal samples were collected from 27 wildlife species in three areas of Sichuan Wolong National Natural Reserve in southwestern China. The subtype (ST) genetic characteristics and prevalence of Blastocystis were determined by PCR amplification of the barcode region (a fragment of ∼600 bp) of the SSU rRNA gene, and phylogenetic analysis were further performed to determine the genetic characteristics of Blastocystis subtypes.Results: 30 of 300 faecal samples (10.0%) were Blastocystis-positive. The highest prevalence of Blastocystis was found in Yinchanggou (18.3%), which was significantly higher than that in Niutoushan (7.5%), and Genda (5.5%) (P < 0.05). Specifically, the highest prevalence of Blastocystis was found in primates (20.0%, 1/5), followed by rodentia 14.3% (1/7), artiodactyla 13.1% (26/198), carnivora 2.3% (2/87), galliformes 0% (0/3). Sequence analysis showed 5 subtypes (ST1, ST3, ST5, ST13, and ST14), with ST13 and ST14 as the predominant subtype (33.3%, 10/30), followed by ST1 (20.0%, 6/30).Conclusions: To the best of our knowledge, this is the first molecular investigation on Blastocystis infection in wild animals in southwestern of China. ST1, ST3, and ST5 were identified in both humans and wild animals, suggesting that these wild animals may be potential reservoirs of Blastocystis for human infection.