Fusarium oxysporum f. sp. lycopersici attacks tomato plants and causes wilt disease. Fusarium Pathogenicity is including pectinases enzymes which enable the Fungal penetration into host cell wall. The present study is focused on using Computational tools such as Auto-Dock program for screening of inhibitors of endo and exopolygalacturonase enzymes. It based on Lamarckian Genetic Algorithm (LGA) that estimate the binding energy and inhibition constant as parameters to select the best binding. The binding energy and amino acids interactions for the selected inhibitors were compared with that of the enzyme substrate (polygalacturonic acid) Allium species such as onion plant have been used widely as antimicrobial and antifungal plants. It contains  ranged  between 1 and 5 %  of non-protein sulfur amino-acids, including SE-Prop-1-enyl-L-cysteine S-oxide, S-3Allylsulphinyl-L-alanine and S-Methylcysteine sulfoxide have satisfactory binding interactions and inhibition constant with endo and exopolygalacturonase. In the present study, these compounds were extracted from white onion bulb Giza 20 and detected in the onion extract LC/MS analysis. The Inhibitory effect of these compounds for exopolygalacturonase enzyme was confirmed experimentally by determination of the enzyme activity in the presence and the absence of these compounds. White onion extract 45% inhibition percentage of the exopolygalacturonase activity. The enzyme kinetic study showed increase in the Km value with  stable V-max value in presence of 7µg/µL of  the onion extract. Also, In-vitro experiment of inhibition of F. oxysporum growth in presence 20% and 40% of onion extract showed inhibition percentages of 47% and 53% respectively. The results concluded that onion extract inhibits Fusarium growth through inhibition of exo and endo polygalacturonase. The inhibitory effect of onion extract could be due to its contents of S-E-Prop-1enyl-L-cysteine S-oxide, S-3-Allylsulphinyl-Lalanine and S-Methylcysteinesulphoxide, these compounds have excellent binding interactions and inhibition effects on both exo- and endopolygalacturonases enzymes of Fusarium   oxysporum f. sp. Lycopersici