Inhibition effect of two essential oils, clove and tea tree oils, on Aspergillus flavus were investigated. Agar disk diffusion, agar plate diffusion plate and fungi –substrate contact methods are three different plating methods for applying tested materials. All used methods confirmed the inhibition effect of clove and tea tree oils on A. flavus growth. Minimum inhibitor (MIC) concentration analysis revealed that 10µl/ml of clove oil and 4 µl/ml of tea tree oil induced a complete inhibition of A. flavus growth. Reduction in the production of reduced sugar indicates to the reduction of analytical activity of A. flavus treated with both used oils. Quantitative analysis of two pectinases encoded genes (Pec-A and Pec-B) indicated to the reduction in the transcript amount of both genes as a result of treatment with both oils. Obtained results pointed to the promising role of clove and tea tree oils as good strategy in controlling A. flavus infection.