<i>Enterocytozoon</i> is a genus of microsporidian parasites, with <i>Enterocytozoon bieneusi</i> being a well-known species. It infects various mammalian hosts, including humans, and exhibits zoonotic potential. Out of the 97 fecal and intestinal samples collected from wild raccoon dogs in Korea, 12 (12.4%) tested positive for <i>E. bieneusi</i> via PCR, revealing 2 genotypes: genotype D and EbpA. Both genotypes were found to belong to the zoonotic Group 1. Notably, this study is the first to report the EbpA genotype in Korea. Although studies on <i>E. bieneusi</i> in raccoon dogs are relatively limited, the findings suggest potential public health concerns.