Evolutionary patterns of sequence divergence were analyzed in genes from the fungal genus Botrytis (Ascomycota), encoding phytotoxic proteins homologous to a necrosis and ethylene-inducing protein from Fusarium oxysporum. Fragments of two paralogous genes (designated NEP1 and NEP2) were amplified from all known Botrytis species and sequenced. NEP1 sequences of two Botrytis species contain premature stop codons, indicating that they may be non-functional. Both paralogs of all species encode proteins with a remarkably similar predicted secondary structure, however, they contain different types of post-translational modification motifs, which are conserved across the genus. While both NEP genes are, overall, under purifying selection, we identified a number of amino acids under positive selection based on inference using maximum likelihood models. Positively selected amino acids in NEP1 were not under selection in corresponding positions in NEP2. The biological significance of positively selected residues and the role of NEP proteins in pathogenesis remain to be resolved.