Wood ear mushrooms (Auricularia heimuer) are commercially used in various fields in South Korea. Therefore, it is necessary to take appropriate measures, including monitoring and prevention of microbial growth in cultivation houses, as microorganisms can reduce the wood ear mushroom’s marketability and cause food poisoning among consumers. Therefore, this study was conducted to evaluate the direct impact of airborne fungi isolated and identified from the indoor air of domestic wood ear mushroom cultivation houses on the mycelia growth of wood ear mushroom strains. For the evaluation, 11 airborne fungal species were tested with three strains of A. heimuer on PDA using the cocultivation method. Among them, Alternaria alternata, Cladosporium anthropophilum, Cochliobolus kusanoi, Lecanicillium sp., Periconia byssoides, and Periconia pseudobyssoides suppressed the mycelial growth of all three A. heimuer strains. There was no significant difference in the reaction against the 11 tested airborne fungal species among the three A. heimuer strains. The results of this study show that proper management of airborne fungi is necessary in the indoor environment of wood ear mushroom cultivation houses.