Edible mushrooms are a sustainable source of unique bioactive metabolites, including antifungal compounds. We investigated antifungal activities of the water or methanol extracts of the medicinal mushrooms Antrodia cinnamomea, Agaricus blazei and Ganoderma spp. against yeast (Candida albicans) and filamentous (Aspergillus fumigatus) fungal pathogens. In the zone of inhibition bioassay, only the methanol extracts of A. cinnamomea (AcM) exhibited potent antifungal activity against C. albicans and A. fumigatus. Resistance testing also indicated that two Penicillium expansum antioxidant mutants were tolerant to the conventional antifungal agent, fludioxonil. P. expansum antioxidant mutants also showed tolerance to AcM. Results indicated that the AcM antifungal action is mediated via the normal antioxidant signaling system present in fungi, where the antioxidant mutants escape the toxicity triggered by AcM. In a benzoic analog bioassay, P. expansum mutants showed similar type of tolerance to the benzoic derivative, thus indicating the presence of natural ingredients in AcM, such as benzoic compounds, could negatively affect the efficacy of AcM when antioxidant mutants are targeted. Thus, AcM could be developed as an effective antifungal agent; however, caution should be exercised in its use of AcM as an antifungal compound so as not to trigger the development of resistance of antioxidant mutants to the treatment.