The present study was undertaken to investigate the effects of using different extracts of two types of trees (Jatropha curcas seeds and Taxodium distichium cones). The solvents used were distilled water and ethanol. The determination of bioactive components of each extract was carried out using gas chromatography/mass spectrometry (GC/MS) analysis. In general, ethanolic extract was more effective on both linear growth and sclerotial numbers and mycelium characteristics of Sclerotium cepivorum than either of the cold or hot water extracts compared to control. Under in vitro conditions, treated with 20% ethanol solvent showed a fungicidal effect. Meanwhile, fungistatic effects appeared at 5% for reduction of mycelium growth. In the greenhouse experiments, the results indicated that onion transplants treated with ethanolic extract of taxodium and jatropha at 20% resulted in a significant reduction in the disease with a significant increase in bulb yield compared with control treatments. This report is one of the few papers that uses taxodium cones and jatropha seeds as antifungal substances against plant pathogens, especially S. cepivorum under worldwide and Egypt conditions.