The antifungal activity of botanical compounds known for this property was tested on two mycotoxigenic fungi contaminating wheat: Aspergillus westerdijkiae and Fusarium graminearum. The reduction of fungal growth was checked through in vitro screening tests on fungi grown on liquid culture medium in 96- or 24-well microtitration plates. The potential of fungal growth reduction was tested for five phenolic acids, 17 terpenic compounds and eight other substances targetting oxidative metabolic chain in mitochondria. The compounds were introduced in the culture medium at a dose range from 1 µL.L-1 to 1 mL.L-1. Fungal biomass production was assessed after 4 d incubation at 25°C through spectrophotometric measurements, either absorbance measurement or fluorescence readings through fungal cell viability test with Alamar blue reagent. Mycotoxin production was determined after 10 d or 21 d culture for F. graminearum and A. westerdijkiae respectively, by HPLC-DAD. The LC50 and LC99 (= MIC) were determined for the most active compounds. The phenolics had very different activities on the two fungal species: F. graminearum was found unsensitive to chlorogenic acid and highly sensitive to trans-cinnamic acid, meanwhile it was the opposite with A. westerdijkiae. Aspergillus westerdijkiae was observed more sensitive than F. graminearum to terpene compounds. Unpurified clove oil extract and linalool induced a highly significant growth reduction on both fungi. Among the third group of compounds, allyl- and methyl-isothiocyanate shown a remarkable antifungal activity on both fungi. There was not observed any increase in mycotoxin production neither on treated cultures of F. graminearum nor of A. westerdijkiae. Fluorimetric measurements improve the accuracy of IC50 and MIC assessment. The Alamar blue assay with fluorometric reading was shown a reliable rapid method to screen for antifungal activity of new candidate biomolecules for biocontrol of mycotoxigenic molds infecting cereal crops or stored grain.