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Background Blastocystis  is an anaerobic unicellular protist frequently detected in the gastrointestinal tracts of humans and animals worldwide. However, the prevalence and subtype distribution of  Blastocystis  in the coypu ( Myocastor coypus ) population have not been reported so far. The aim of this study was to determine the prevalence, genetic characteristics, and zoonotic potential of  Blastocystis  isolates detected in coypus in China. Results A total of 308 fecal samples were collected from coypus in seven regions across China and subsequently examined.  Blastocystis  was detected in 44 (14.3%) specimens by nested PCR amplification of the small subunit ribosomal rRNA (SSU rRNA) gene. Further DNA sequencing and phylogenetic analyses resulted in the identification of two zoonotic known subtypes, ST4 and ST5, and an unknown subtype. ST4 was the most predominant subtype observed in the samples. ST5 infections were only observed in three coypus. Factors that were associated with prevalence of  Blastocystis  included age, geographical region and subtype. Interestingly, this is the first report about a potentially novel subtype infecting coypus. Conclusions This is the first comprehensive report of  Blastocystis  in  M. coypus  across a wide geographic range of China. A moderate degree of genetic divergence was observed. The presence of zoonotic subtypes in farmed  M. coypus  suggests that these animals have the potential to transmit blastocystosis to both humans and domestic animals. These findings provide a better understanding of the genetic diversity of  Blastocystis  in rodents and contribute towards the establishment of efficient blastocystosis control strategies in the investigated areas. Graphical abstract

Occurrence and subtyping of Blastocystis in coypus (Myocastor coypus) in China