Border disease virus (BDV) of sheep, an important ovine pathogen, is serologically related to the two other well characterized members of the Pestivirus genus of the Flaviviridae family, namely bovine viral diarrhea virus (BVDV) and hog cholera virus (HoCV). To determine its genetic relationship to BVDV and HoCV, the genome of BDV strain, BD-78 encompassing the 5' untranslated region (UTR) and structural gene coding region was molecularly cloned and the nucleotide sequence determined. The sequenced region of 3,567 nucleotides contained one open reading frame encoding 1063 amino acids. The nucleotide and amino acid sequences of BD-78 were compared with those of two BVDV strains NADL and SD-1, and the Alfort and Brescia strains of HoCV. The overall nucleotide sequence homologies of the region sequenced of BD-78 are 68.3% with BVDV-NADL, 67.8% with BVDV-SD-1, 69.0% with HoCV-Brescia, and 65.8% with HoCV-Alfort. The overall amino acid sequence homologies of BD-78 are 76.1% with NADL, 76.5% with SD-1, 74.2% with Brescia, and 72.9% with Alfort. The most conserved nucleotide and amino acid sequences between BD-78 and the other pestivirueses are in the 5' UTR and the capsid protein coding region (p14), where as the most divergent sequences are in the E2 coding region. These findings suggest that BDV is a unique virus in the Pestivirus genus.