This study was conducted to survey the fungal microorganisms that cause common diseases and reduce the quality of onion bulbs produced in Assiut and Sohag governorates in Egypt, particularly Botrytis Brown Stain (BBS) disease on onion bulbs. Aspergulls niger, A. flavus, Penicillium oxalicum, Botrytis allii and B. cinerea strains were isolated from onion. B. cinerea was the strain that clearly showed brown spot symptoms while other tested fungal strains did not show significant symptoms. The highest severity of 52.00% was found for B. cinerea. Eucalyptus(Eucalyptus chamadulonsis), Bitter apple(Citrullus colocynthis), and Neem (Azadiratcha indica) aqueous plant extracts were used and their ability to reduce the growth of the fungal pathogen. The extract of Bitter apple(Citrullus colocynthis) at concentrations of 5 and 10% resulted in the highest growth inhibition by 13.33 and 8.89%, respectively. The plant extracts ability to reduce the disease severity on onion bulbs under storage condition were evaluated. The C. colocynthis plant extract exhibited significantly increased of the total phenolic and salicylic acid contents in onion plants compared to untreated plants. The results also indicated that C. colocynthis plant extract was the most effective and comparable with the recommended fungicide. Therefore, the natural plant extracts can be recommended as alternative to highly toxic and expensive fungicides.