Genus Metagonimus has been a subject of taxonomic debates for several years. In morphological aspects, M. yokogawai has been thought to have three subtypes, namely Yokogawa type (M. yokogawai in strict sense), Miyata type and Koga type, But differences in the intestinal pathology induced by these subtypes have not been studied yet. In this study we compared the pathological reactions induced by M. yokogawai and Metagonimus Miyata type using proliferating cell nuclear antigen (PCNA) index. Metacercariae (Mc) of M. yokogawai were collected by artificial digestion of Plecoglossus altivelis and Mc of Metagonimus Miyata type were collected from Zacco platypus. Three hundreds Mc of each species were infected orally to ICR mice. The mice were sacrificed at 3, 6, 10, 16 and 23 days after infection and the small intestines were resected into three portions (proximal, middle, and distal). Immunohistochemical staining for PCNA was done using PC-10 (DAKO-PCNA, CA, USA). The PCNA indices in M. yokogawai infected group on the 6th and 23rd day after infection were lower than in the control and Miyata type infected groups (p < 0.05) from all of the three intestinal regions. On the other hand, the control group and Metagonimus Miyata type infected group did not make any differences in PCNA indices. The villus/crypt (V/C) ratio was also decreased significantly in M. yokogawai infected mice but not in Metagonimus Miyata type infected ones. It is suggested that M. yokogawai induce villous atrophy through a decrease in the cell proliferation at the crypt. The results of this study suggested that M. yokogawai induce more serious intestinal pathology than Metagonimus Miyata type.