The potential use of allyl isothiocyanate (AITC) and ethyl isothiocyanate (EITC), singly and in combination, was tested in in vitro and in vivo trials for their effect on Penicillium expansum Link and Botrytis cinerea Persl. infection on apple when used as a fumigant. A 3 : 1 ratio of AITC : EITC was more efficient at reducing in vitro spore germination of P. expansum and B. cinerea than were other combinations or either AITC or EITC alone. The optimized combination showed the lowest EC50 values, at 0.08 and 0.14 μg/ml air, for P. expansum conidial germination and mycelial growth, respectively, and 0.07 and 0.12 μg/ml air for B. cinerea conidial germination and mycelial growth, respectively. In in vivo trials, artificially infected apples were exposed for 4 days to an ITC‐enriched atmosphere. Among the ITCs tested, AITC, EITC and their combinations reduced incidence by more than 85% after 3–4 days of apple incubation at 20°C. Although further studies are necessary to evaluate any detrimental effects on apple quality, the evidence from this study supports the use of fumigation based on ITCs, and in particular a 3 : 1 combination of AITC and EITC, for control of postharvest mildew in apple fruit.