Soil fumigation with the synthetic essential oil of mustard (93% allyl isothiocyanate) (EOM) was evaluated as a substitute of bio-fumigation with cruciferous plant species, using Sclerotium rolfsii and Sclerotinia sclerotiorum as test pathogens, together with its non-target effect on the general population of soil microorganisms. The mortality of the sclerotia of both fungi was dependent upon the concentration of EOM and the exposure period. Exposure to the EOM vapors delayed in vitro germination of the sclerotia. Total germination of the control sclerotia of S. rolfsii, after 120 h incubation, was 94%, of which 88% germinated within 48 h. In contrast, to the total germination of 77% or 47%, less than 3% germinated in 48 h when exposed for 4 or 7 days to 50 µl EOM/L. Exposure to 100 µl/l for 4 or 7 days resulted in the mortality of 50 and 100% sclerotia, respectively. The tendency for delayed germination and mortality was similar for the sclerotia of S. sclerotiorum. No viable sclerotia of either fungus were detected to the depth of 10 cm in the air dried, moist or wet soil fumigated for 7 days with the EOM at the rate of 150 µl/L. In the field plots, no viable sclerotia of S. rolfsii were detected after 7-day exposure to the EOM applied to the upper soil layer at the rate of 9, 12, or 18 ml/m 2 and covered with a plastic sheet, while 73, 50 and 15%, respectively, were recovered from uncovered plots. In field plots, the fluorescein diacetate hydrolysis decreased by EOM treatment. However, the colony forming units of actinomycetes and bacteria increased, but those of fungi decreased significantly. Soil fumigation with EOM can be used with several advantages, as a substitute of bio-fumigation with cruciferous plant species.