In human fasciolosis, differential diagnosis of the causative flukes, Fasciola hepatica and Fasciola gigantica, is problematic. We report a rare case of human fasciolosis in which an adult worm was recovered from the bile duct of a Japanese man. Morphometric data of the worm were consistent with those of F. hepatica, whereas the size of eggs in the stool indicated infection with F. gigantica. Nucleotide sequences of ITS-1 and -2 and CO1 genes of the DNA extracted from the eggs revealed that the genotype was that of F. hepatica. These findings suggest that the size of eggs is not a suitable marker for species identification in human fasciolosis, especially in settings such as the East Asian region where different karyotypes and hybrid genotypes of F. hepatica and F. gigantica have been found.