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This study describes the activity-guided isolation and purification of antimicrobial proteins from the seeds of Foeniculum vulgare. Purification was carried out by (NH4)2SO4 precipitation, gel filtration and ion-exchange chromatography. Antifungal and antibacterial activities were determined by disc diffusion assay method. SDS-polyacrylamide gel electrophoresis revealed that the purified protein was a monomer with molecular mass of 60 kDa. This is a first report on purification of a protein from Foeniculum vulgare, which possesses a strong and broad spectrum antimicrobial activity. Our results suggest that the antimicrobial properties of this plant seed may be further investigated to explore the possibility of using them in the treatment of candidal or bacterial infections.