Five strains were isolated and purified from moldy cigarettes, and were identified by fungal morphology and microscopy. It was found that there were 2 strains of Aspergillus, 1 strain of Penicillium, 1 strain of Alternaria, and 1 strain of Cladosporium. Through the 18S rDNA-ITS sequence analysis and the construction of phylogenetic tree, the mildew microorganism of cigarettes were identified as five species, such as Aspergillus sydowii, Aspergillus flavus, Cladosporiumtenuissimum, Penicilliumdigitatum and Alternaria. It was concluded that Aspergillus flavus was the main strain causing mildew in cigarette products by the mildew experiment.