Local clustering of HCV infection has been reported in various regions in Japan. We investigated the transmission of HCV in this region constructioning a phylogenetic tree. Methods: HCV genotypes (Okamoto) were compaired among HCV-infected individuals in Saga Prefecture, Japan, in the districts with a high seropositivity rate for antibodies to HCV (H district) and a low seropositivity rate (L district). A phylogenetic tree was constructed based on the HCV genomic sequences, using a neighbor-joining method. Results: The prevalence of genotype II was significantly higher in the H district (45, 90%) than in the L district (19, 52.8%; p<0.001). Almost 20 strains of HCV genotype II from the H district were clustered in the same region of the phylogenetic tree. Conslusions: These results suggest that an increase in transmission of similar strains of HCV occurred previously in the H district, and so we found large differences in HCV seropositivity and distribution of genotypes between the H and L districts.