Plant polygalacturonase inhibitor proteins (PGIPs) bind fungal polygalacturonases (PGs), but inhibition specificities and kinetics vary within and among species. Purified bean PGIP inhibited all fungal PGs we tested, including Fusarium moniliforme PG. Pear PGIP, however, was only effective against Botrytis cinerea PG. Moreover, tomato PGIP inhibited B. cinerea PG more than Aspergillus niger PG. Models of codon evolution for 22 dicot PGIPs and 19 fungal PGs indicated that advantageous substitutions dominate the molecular evolution of these genes and identified 9 amino acid residues, each, that are likely to evolve adaptively in response to natural selection. Many of these residues are within the β-strand/β-turn region of the PGIP LRR, including two sites known to alter inhibition specificities of bean PGIPs, but others lie outside this region. Our results complement existing molecular and biochemical studies of resistance specificity, and suggest new target amino acids for manipulating PG-inhibition. (C) 2000 Academic Press.