Phylogenetic analyses of bovine viral diarrhea virus (BVDV) were performed based on the nucleotide sequences of the 5' untranslated region (5'-UTR) and E2-coding gene. Thirty-six BVDV detected from naturally infected cattle in the northern region of Japan were divided into three genotypes, BVDV1a, BVDV1b and BVDV2, in a 5'-UTR phylogenetic tree. In a phylogenetic tree constructed from the E2-coding gene, BVDV1c was identified and the viruses classified in BVDV1c were included in BVDV1a in the 5'-UTR phylogenetic tree. Moreover, BVDV1a and BVDV1b in the E2-phylogenetic tree clustered closer together than in the 5'-UTR tree. These results suggested that phylogenetic analysis of the E2 gene was more useful for identification of subgenotypes within BVDV1.