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The present study aimed to investigate the inhibition of in-package aerosolized aqueous antimicrobials against postharvest black mold caused by Aspergillus niger (A. niger) on apple fruit and in maintaining fruit quality. Apple fruit is susceptible to A. niger infection during storage, resulting in a significant decline in its quality. In this paper, the ability of chlorine dioxide (ClO2), Epsilon-polylysine (ɛ-PL), hydrogen peroxide (H2O2) and ozone (O3) to prevent and control Aspergillus infection in postharvest apples was evaluated. Results indicated that the treatments of 400 mg L−1ClO2, 500 mg L−1 and 1000 mg L−1 ɛ-PL could effectively alleviate the severity of postharvest black mold (A. niger) of apples and inhibit mycelial growth of A. niger. In addition, 0.5 mg L−1 O3 and 5% H2O2 also inhibited the mycelial growth of A. niger in treated apples. Further studies indicated that aerosolized ClO2 and e-PL increased corresponding defense-related enzyme activity and produced higher phenolic levels to improve disease-resistant of apples. Moreover, aerosolized ClO2, e-PL, H2O2 and O3 could be effective for maintaining quality of apple fruit during 24 days of storage at 20 °C. The present study gives a first insight into the A. niger control effect of in-package aerosolization technology associated with antimicrobials, which may be a potential method for the inhibition of A. niger on apple fruit.