Bovine viral diarrhoea virus 2 (BVDV-2) strains demonstrated in cattle, sheep and adventitious contaminants of biological products were evaluated by the palindromic nucleotide substitutions (PNS) method at the three variable loci (V1, V2 and V3) in the 5’ untranslated region (UTR), to determine their taxonomic status. Variation in conserved genomic sequences was used as a parameter for the epidemiological evaluation of the species in relation to geographic distribution, animal host and virulence. Four genotypes were identified within the species. Taxonomic segregation corresponded to geographic distribution of genotype variants. Genotype 2a was distributed worldwide and was also the only genotype that was circulating in sheep and cattle. Genotypes 2b, 2c and 2d were restricted to South America. Genotypes 2a and 2d were related to the contamination of biological products. Genetic variation could be related to the spread of BVDV-2 species variants in different geographic areas. Chronologically, the species emerged in North America in 1978 and spread to the United Kingdom and Japan, continental Europe, South America and New Zealand. Correlation between clinical features related with isolation of BVDV-2 strains and genetic variation indicated that subgenotype 1, variant 4 of genotype 2a, was related to a haemorrhagic syndrome. These observations suggest that the evaluation of genomic secondary structures, by identifying markers for expression of virus biological activities and species evolutionary history, may be a useful tool for the epidemiological evaluation of BVDV-2 species and possibly of other species of the genus Pestivirus.