A study of molecular diversity was carried out on 136 sugar beets infected with Beet necrotic yellow vein virus (BNYVV, Benyvirus) collected worldwide. The nucleotide sequences of the RNA-2-encoded CP, RNA-3-encoded p25 and RNA-5-encoded p26 proteins were analysed. The resulting phylogenetic trees allowed BNYVV to be classified into groups that show correlations between the virus clusters and geographic origins. The selective constraints on these three sequences were measured by estimating the ratio between synonymous and non-synonymous substitution rates (omega) with maximum-likelihood models. The results suggest that selective constraints are exerted differently on the proteins. CP was the most conserved, with mean omega values ranging from 0.12 to 0.15, while p26 was less constrained, with mean omega values ranging from 0.20 to 0.33. Selection was detected in three amino acid positions of p26, with omega values of about 5.0. The p25 sequences presented the highest mean omega values (0.36-1.10), with strong positive selection (omega=4.7-54.7) acting on 14 amino acids, and particularly on amino acid 68, where the omega value was the highest so far encountered in plant viruses.