Grain samples of Cicer arietinum (Chickpea), Zea mays (Maize), Cajanus cajan (Pigeon pea), Hordeum vulgare (Barley), Oryza sativa (Rice) and Sorghum vulgare (Millet) were procured from various retailers of market were subjected to their mould profile. During mycoflora analysis, 1297 fungal isolates were recorded from the food commodities. The least number of fungal isolates (189) were detected from H. vulgare while highest (244) from Z. mays. The genus Aspergillus was found to be most dominant encountered in all the samples, followed by Cladosporium cladosporoides, Alternaria alternata and Penicillium species. The highest percent relative density was recorded in case of Aspergillus flavus (36.24) followed by A. niger (28.45) and C. cladosporoides (10.95) while the lowest was found in case of Trichoderma viride (1.16). Some of the A. flavus isolates were toxigenic secreting aflatoxin B 1 . The survey reveals that the contamination of food commodities with storage fungi and mycotoxin is alarming and appropriate quality control measures should be taken urgently. The essential oil of Thymus vulgaris L. showed highest antifungal efficacy. The thyme oil absolutely inhibited the mycelial growth of A. flavus at 0.7µl ml -1 . The oil also showed significant antiaflatoxigenic efficacy as it completely arrested the aflatoxin B 1 production at 0.6µl ml -1 . Thyme oil as fungitoxicant was also found superior over most of the prevalent synthetic fungicides. The findings recommend the thyme oil as potential botanical preservative in eco-friendly control of biodeterioration of food commodities during storage.