Different types and subtypes of bovine herpesvirus 1 and 5 (BoHV-1 and BoHV-5) have been associated to different clinical conditions of cattle, in such a way that type/subtype differentiation has become an essential tool for understanding the pathogenesis and epidemiology of BoHV infections. In search for a genomic region that would allow a clear distinction between BoHV-1 and BoHV-5, the carboxy-terminal portion of glycoprotein C (gC), corresponding to residues 321-450 (BoHV-1) and 301-429 (BoHV-5) of 23 South American (SA) isolates (Brazil mostly) was amplified and sequenced. The nucleotide sequence alignments revealed levels of genomic similarity ranging from 98.7 to 99.8% among BoHV-1 isolates, 88.3 to 92% between BoHV-1/BoHV-5 and 96 to 99.7% among BoHV-5 isolates. At the amino acid level, sequence similarity varied ranging from 97.5 to 99.5% among BoHV-1, 77.5 to 84.4% between BoHV-1/BoHV-5 and 92.1 to 99.5% (BoHV-5/BoHV-5). The isolates could be clearly separated into BoHV-1.1, BoHV-1.2 and BoHV-5 after phylogenetic analysis. The results suggest that the phylogenetic analysis performed here can be used as a potential molecular epidemiological tool for herpesviruses.