Blackberry yellow vein disease (BYVD), a disorder caused by virus complexes, has become a major threat to fresh market blackberry production in the United States. Blackberry yellow vein associated virus (BYVaV) is the most prevalent virus in the BYVD complexes; detected in about 50% of samples exhibiting typical disease symptoms. Thirty-four virus isolates infecting wild and cultivated blackberries were collected from several areas with high BYVD incidence. Sequence variability and virus evolution predictions were calculated for four genomic regions coding for six proteins and accounting for about 30% of the virus genome. Nucleotide diversity ranged between 7 and 12%, and all proteins studied were under negative selection. Several isolates were identified as potential recombinants suggesting that recombination might be a driving force behind BYVaV evolution.