An antimicrobial protein from seeds of Pharbitis nil (Pn-AMP) which shows an antifungal activity towards several agriculturally important plant pathogens has been crystallized in the presence of equimolar N-acetylglucosamine with sodium citrate as precipitant. The crystal belongs to the hexagonal space group P6122 (or P6522), with unit-cell parameters a = b = 29.33 (5), c = 133.44 (12) A. Native data were collected using a crystal at 100 K to a resolution of 1.78 A.