Fusarium wilt disease is one of the major plant diseases that affect tomato production. The effects of neem (Azadirachta indica) and willow (Salix babylonica) aqueous extracts on fusarium wilt disease in tomato seedlings were investigated. Four weeks old tomato seedlings were treated with 10% of either neem and willow aqueous extracts and then infected with Fusarium oxysporum after 4 days of treatment. The results showed that the percentage of disease incidence was increased in non treated tomato seedlings in time dependent manner and reached the maximum level (65%) after 6 weeks of infection. Treatments of tomato plants with neem and willow aqueous extracts reduced the percentage of disease incidence to the level of 25.5% and 27.8% after 6 weeks of infection respectively. The results show that infection of tomato seedling with Fusarium oxysporum led to many morphological and biochemical changes including, reducing the growth of tomato shoot and root, increasing the level of lipid peroxidation and marked increase in the activities of antioxidant defensive enzyme i.e. POX, CAT, and SOD. Treatment with neem and willow aqueous extracts significantly exhibited a growth promotion of tomato shoot and root in infected or non infected seedling. Moreover, application of neem and willow aqueous extracts with fusarium, significantly reduce the level of lipid peroxidation and induce high activities of antioxidant defensive enzymes after 3 and 7 days of infection. Electrophoretic pattern of POX demonstrated that Fusarium oxysporum caused up regulation of several POX isoenzymes. It could be concluded that neem and willow aqueous extracts reduced the disease incidence of fusarium wilt in tomato seedlings by increasing the activities of antioxidant defensive enzymes and decreasing the level of lipid peroxidation.