Botrytis cinerea species complex (BCSC), the causal agent of gray mold disease, is one of the most common diseases of the storage in fruits such as apples, pomegranate, kiwi, strawberries, stone fruits, grapes, etc., and could be causes a lot of damage in the post-harvest stage. Clove oil, in addition to clinical and medical applications, is also recommended for the control of fungal infectious agents. In this study, after sampling at ten cold storages in different regions of the country, isolation and morphological and molecular studies of the isolates, the level of effectiveness of the organic Clove Oil (BIOXEDA) was measured and evaluated with chemical fungicide (Thiabendazole) and the control sample. The concentrations of 0 (control), 1000, 2000, and 3000 μl of organic clove oil and chemical fungicide added to 1000 ml of PDA medium autoclaved in three replicates. The rings from the margin of the growing colony of B. cinerea were transferred on petri dishes containing essential oil and chemical fungicide to evaluate the efficacy of these compounds in comparison with the control sample and identify appropriate concentrations for control this causal agent. Finally, after six days, B. cinerea grew up to 70 mm on the control treatment and fully covered the petri dish. The fungus did not germinate and grow on the organic treatment of clove oil at concentrations of 1000, 2000 and 3000 μl / liter, and couldn't produce colony. Meanwhile, the fungus grown on the treatment of thiabendazole between 30 to 60 mm. The results showed a significant difference in the effect of clove oil on control and prevention of germination and growth of B. cinerea in comparison with the chemical treatment of thiabendazole and control. Therefore, the use of this organic, healthy and environmentally friendly material is recommended to control the disease and reduce the amount of gray mold damage in the fruit industry