Citrus limon (lemon) is a widely cultivated citrus fruit. Significant postharvest losses due to fungi plague its production. Environmental and human health hazards have made the application of synthetic fungicides unsuitable. Despite the previous reports of antifungal activities of essential oil (EO) vapors, their synergistic combinations are understudied. Synergistic vapor combinations are advantageous due to less concentration of active components. This study aimed to isolate and identify postharvest fungal pathogens lemon and to evaluate the antifungal effects of synergistic Monarda citriodora EO (MEO)-constituent vapor combinations in vivo and in vitro. Postharvest fungal pathogens of lemon (C. limon) were isolated from various infected samples. The most pathogenic isolate was identified through morphology and its ITS-based rRNA gene sequencing as Aspergillus foetidus (O4). This is the first report of A. foetidus as a postharvest pathogen of lemon. The minimum fungicidal concentrations (MFCs) of MEO vapors treatment against O4 were 1346.15µL/L air. For carvacrol, hexanal, and linalool, MFC was same (96.16µL/L air). Checkerboard assays demonstrated that 1/4 MFC of MEO (336.54µL/L air) and 1/4 MFC of linalool (24.04µL/L air) (M+L) were synergistic against O4. M+L vapors reduced the O4 growth on lemons during storage by 64%±1.50% and preserved their quality (low weight loss %, unchanged pH, increased ascorbic acid content). Propidium iodide staining, ergosterol content analysis, calcofluor white staining and chitin content analysis revealed the integrity loss of the O4 plasma membrane and cell wall. 2',7'-Dichlorofluorescin diacetate staining revealed accumulation of intracellular reactive oxygen species (ROS), and scanning electron microscopy (SEM) analysis exposed the M+L treated mycelia with malformations. M+L vapors offer protection for lemons from A. foetidus and preserve their quality during storage.