Enterocytozoon is a genus of microsporidian parasites, with Enterocytozoon bieneusi 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 E. bieneusi 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 E. bieneusi in raccoon dogs are relatively limited, the findings suggest potential public health concerns.