An apple polygalacturonase-inhibiting protein (PGIP), which specifically inhibits endopolygalacturonase (PG, EC 3.2.1.15) from Botryosphaeria dothidea, was purified from Botryosphaeria dothidea-infected apple (Malus domestica cv. Fuji) fruits. The purified apple PGIP had a molecular mass of 40 kDa. The N-terminal amino acid sequence of the purified protein showed high homologies to those of PGIP from pear (100%), tomato (70%), and bean (65%). We also purified polygalacturonase (PG) from B. dothidea. The PG hydrolyzes pectic components of plant cell walls. When the extracted apple pectic cell wall material was treated with purified apple PGIP and B. dothidea PG, the amount of uronic acid released was lower than that treated with B. dothidea PG alone. This result demonstrates that PGIP functions specifically by inhibiting cell wall maceration of B. dothidea PG Furthermore, we characterized the de novo function of the PGIP against PG on the solubilization and depolymerization of polyuronides from cell wall of apple fruits inoculated with B. dothidea. This result demonstrated that the PGIP of plants exhibits one of the direct defense mechanisms against pathogen attack by inhibiting PGs that are released from pathogens for hydrolysis of cell wall components of plants.