Until now, 3 Metagonimus spp. (M. yokogawai, M. takahashii, and M. miyatai) causing human metagonimiasis have been reported in Korea. In this study, we investigated the possible presence of Metagonimus spp. other than these 3 species using human fecal samples from an endemic area in Korea. DNA was extracted from Metagonimus egg-positive fecal samples collected from residents of Gurye-gun, Jeollanam-do. A total of 21 representative mitochondrial cytochrome c oxidase subunit I sequences were obtained by PCR and cloning, and sequencing. Phylogenetic analysis revealed 1 cluster corresponding to M. yokogawai (n=10) and 2 additional distinct clusters corresponding to M. kogai (n=8) and M. saitoi (n=3), which were proposed as new species in Japan in 2022. Pairwise cytochrome c oxidase subunit I distances were low for M. yokogawai and M. kogai (mean Kimura 2-parameter: 0.005–0.006), whereas M. saitoi showed higher Korea–Japan values (~0.029), a pattern consistent with geographic structuring. In conclusion, we provide the first molecular evidence for the occurrence of M. kogai and M. saitoi in human fecal samples in Korea. Further confirmation using adult morphology, additional nuclear markers, and ecological surveys are needed to clarify metagonimiasis transmission in the Seomjin-gang (river) basin.