Background and Aim: Aflatoxins which are mainly produced by Aspergillus parasiticus are among the highly toxic secondary metabolites. This species often contaminates food and agricultural products including cereals, peanuts, and crops in the field. Recently, a number of studies have been carried out on the elimination of aflatoxin, and the antifungal effects of medicinal herbs, such as Chenopodium album  (36HYU2385) and Apium nodiflorum (36HYU2362). In this study, the effects of C. album and A. nodiflorum as natural compounds were examined on Aspergillus parasiticus growth, aflatoxins production and the aflR gene expression.Materials and Methods: The antifungal susceptibility testing of C. album and A. nodiflorum were performed according to CLSI document M38-A2. Quantitative changes in aflR gene level of expression were analyzed by Real-time PCR method.Results: Results indicated that minimal inhibitory concentration (MIC) in the extracts of C. album and A. nodiflorum against A. parasiticus growth were 100 mg/ml and 120 mg/ml respectively. Extracts of Chenopodium album and Apium nodiflorum have antitoxic properties. Moreover, they effectively decrease aflatoxin production. The level of aflR gene expression was decreased significantly after the exposure of fungal cells to the extracts. The highest inhibition was observed in MIC= 100 mg/ml of C. album.Conclusion: According to the results, it can be suggested that these herbal extracts may have antifungal potential to be used in medicine or agriculture.