Airborne fungi are one of the major components of aeromycobiota known to produce several fungal diseases in fruits. Their presence in indoor environment of warehouses may limit the storage period of apples. Qualitative and quantitative analysis of airborne fungal spores were conducted using gravity settling techniques to detect fungal airspora present in the atmosphere of two apple warehouses in Tunisia. In this study, 375 fungal isolates were obtained and purified. Phylogenetic analysis of Calmodulin, beta-tubulin and ITS regions coupled with phenotypic characterization helped to identify fifteen fungal species. Penicillium exhibited the highest diversity with ten species detected (Penicillium expansum, Penicillium allii, Penicillium polonicum, Penicillium solitum, Penicillium chrysogenum, Penicillium steckii, Penicillium viridicatum, Penicillium sumatraense, Penicillium italicum and Penicillium citrinum), followed by four species of Aspergillus genus (Aspergillus niger, Aspergillus pulverulentus, Aspergillus flavus and Aspergillus europaeus) and Alternaria alternata. In vivo experiments confirmed the pathogenicity of thirteen species at room temperature and under cold-storage conditions. Among them, A. europaeus, A. pulverulentus, P. allii and P. Sumatraense were described for the first time as pathogenic on apples. The present study identified the major airborne fungi associated with postharvest rot in apple storage facilities in Tunisia and may help in efficient control of post-harvest and storage fruit diseases.