The present study was carried out to investigate the concentration and species diversity of airborne fungi in thermophilic mushroom cultivation houses. Fungal concentration measurements were performed in April and May 2022 for a Pleurotus ostreatus cultivation house, in July and August 2023 for a Pleurotus sajor-caju and Agaricus blazei cultivation house, and in June, July and August 2023 for a Pleurotus pulmonarius, Pleurotus sajor-caju and Calocybe indica cultivation house. The airborne fungal concentration was 2.95 × 102 CFU/m3~105CFU/m3, above 105CFU/m3, and 1.12 × 103 CFU/m3~ 9.17 × 103 CFU/m3 in the three cultivation houses, respectively. A total of 8 genera and 22 species of airborne fungi were isolated from three mushroom cultivation houses. 5 genera and 7 species were identified from P. ostreatus cultivation house. Furthermore, 4 genera 6 species were found from A. blazei and C. indica cultivation house. In addition, 5 genera and15 species were isolated from P. pulmonarius, P. sajor-caju and C. indica cultivation house. Among the fungi isolated, the class of Eurotiomycetes was the most common. Among the 22 fungal species, Aspergillus flavus, A. ochraceus A. sydowii, A. tubingensis, A. westerdijkiae, Penicillium brevicompactum, P. citrinum, and P. steckii have been reported as harmful species to mushrooms, food, and human.