The apple juice is one of the most popular products obtained from apples. The apple juice is know as an antioxidant, antimicrobial and anticancer and has beneficial effects on the human health. A major concern of the apple juice industry is mainly related to the toxigenic and spoiling micro-organisms that can survive the pasteurization condition. The main agent of the apple juice mold spoilage, Byssochlamys fulva, tolerat the pasteurization by producing heat resistant ascospore. Since these ascospores are able to survive routine heat pasteurization applied to many fruit products, spoilage may occur due to post pasteurization germination and subsequent outgrowth. During the recent years, natural antimicrobials have attracted considerable attention due to the increased consumer awareness of the aspects of food quality and safety. The major drawback with antimicrobial components of plant essential oil is their sparing solubility in aqueous phases. The oil-in-water nanoemulsion is such an imperative mean for the delivery of these above mentioned water-insoluble/sparingly-soluble antimicrobials. The purpose of this study was to produce an oil in water nanoemulsion of Zataria multiflora and Carum copticum oil, using the ultrasound waves. The nanoemulsion of each C. copticum and Z. multiflora oil with formulation of 3% sesame oil, 3% Z . multiflora oil, 3% C. copticum oil, 24% Tween 80 as emulsifier and 70% water was prepared, separately. The features of Nanoemulsions were well evaluated by determining turbidity reading the absorbance at 600 nm, the resistance of the nanoemulsion, other particles and poly-dispersity Index (PDI). In order to determine the antifungal properties of the prepared nanoemulsions against Byssochlamys fulva (determining the inhibition percentage), the concentration of the Z.multiflora oil was increased to 4.5 percent and 6 percent in case of the Z. multiflora oil nanoemulsion and in the C. copticum issue the concentration of the oil was increased to 4.5 percent. After 30 minutes of sonication, the absorption rate of the Z. multiflora and C. copticum nanoemulsions was obtained 0.022 and 0.016, respectively. In the visual evaluation made to determine their resistance, it was indicated that in a temperature of 25 °C they maintained their stability for more than six months and o phase separation and creaming were observed in them. The particle size for the C. copticum nanoemulsion was obtained 15.13 nm with a PDI of 0.253 and the particle size of Z. multiflora nanoemulsion was obtained 19.42 nm with a PDI of 0.377. The highest amount (86% and 84.23%) of inhibition were obtained in a concentration of 25 ?l / ml nanoemulsion of 4.5% C. copticum and a concentration of essential oils 5 ?l / ml nanoemulsion of 6% Z. multiflora, respectively. The results showed that at the zero time, (immediately after inoculation of Byssochlamys in the apple juice) no difference was observed between the control and the treatments, but significant difference was observed between the treatments and control during the storage period (p?0/05). The results of the turbidity of the apple juice containing nanoemulsion during a three week period of observance indicated that the significant difference (p?0/05) between the control and the treatment of Z. multiflora nanoemulsion was observed on the fourteenth day, but between the control and the treatment of C. copticum nanoemulsion significant difference was not observed. Results howed that Z. multiflora and C. copticum oils nanoemulsions can be used as antifungal compound in beverages, especially fruit juice industry. Keywords : Nanoemulsion, Zataria multiflora oil, C arum copticum oil, Byssochlamys fulva , ultrasound.