Abstract: To study the diversity of fungi in the air of tobacco warehouses, monthly collection, isolation and identification of fungi in the air of floors 1-5 of 3 warehouses (Dongxiao in Longyan, Hongtanshan in Longyan and Dongfu in Xiamen) were carried out with the air sampling method from January to December in 2019. The results showed that:(1) The fungal quantity in the air of each floor of the three warehouses was high in summer but low in other seasons, and the content of fungi in the air of Dongxiao and Hongtanshan warehouses were higher than that of Dongfu, with the highest value being 10.9 and 9.4 times of Dongfu, respectively. (2) A total of 835 fungal strains, belonging to 3 phyla, 10 classes, 54 genera and 158 species, were obtained from the 3 warehouses. The dominant genera were Penicillium, Cladosporium and Aspergillus. P. Citrinum, P. Corylophilum, C. Halotolerans, C. Cladosporioides and C. Tenuissimum were the species that accounted for more than 10% of the total isolates number in the air of the tobacco warehouses. The results of Venn diagram analysis showed that 68, 92 and 68 species of fungi existed in the warehouses of Dongxiao, Hongtanshan and Dongfu, respectively. 20 species were common to the 3 warehouses, and the numbers of specific species for the warehouses in Dongxiao, Hongtanshan and Dongfu were 26, 45 and 37, respectively. (3) The numbers of fungal species in the air of tobacco warehouses were relatively high in winter, but relatively low in late spring and early summer over a period of one year. C. cladosporioides, C. tenuissimum and P. citrinum were relatively steady fungal species in the air of tobacco warehouses.