During the last two decades, there has been an increase in the demand for fresh and ready to eat foods with high nutritional value and free from preservatives and additives. Pomegranate is a typical fruit which is rich in various antioxidants and vitamins in addition to good aroma and taste and unique sensory characteristics. Common processes of this fruit, such as drying, sauce making, extracting and juicing reduces nutritional value and freshness of pomegranate. On the other hand, the difficulty in peeling and removing the arils has limited its fresh consumption. For this reason, the “ready-to-eat” pomegranate can increase the possibility of fresh consumption of the fruit Pomegranate arils are corruptible and cannot be kept for a long period of time Therefore, with the use of effective solutions, bacterial growth can be prevented and corruptibility of pomegranate arils can be delayed to increase persistency of them. One efficient method to achieve this goal is Modified Atmosphere Packaging (MAP) consisting of essential oils. In this study, modified atmosphere packaging containing Zataria multiflora Boiss was used to increase shelf life of pomegranate arils. For this purpose, 60 g of pomegranate arils together with whatman papers saturated with 0, 100 or 200 Zataria multiflora Boiss were packed in a 100 ?m thick low density polyethylene (LDPE) heat-sealed bags. Each bags had 0, 1 or 3 perforations with 150 ?m in diameter. Some bags were kept for 11 days at 5 ?C and some were kept for 9 days at 15 ?C. During the storage period headspace gas composition and quality parameters including weight loss, drip loss, pH, acidity, TSS, firmness, Antioxidant capacity, color and microbial counts were measured. Statistical analysis of the results of qualitative evaluation of pomegranate aril showed that, number of perforations had significant effect on product weight loss, drip loss and antioxidant capacity, different concentrations of essential oils on respiration, weight loss, driploss and microbial load and temperature and storage time on all qualitative characteristics. Therefore, with decreasing temperature from 15?C to 5?C and increasing the concentration of essential oil from 0 to 200 , the microbial count of product were decreased. On the other hand, in order to predict the qualitative characteristics of the product during storage the mathematical models to describe the kinetics of quality changes as a function of the storage temperature, concentration of essential oil and number of perforations were developed. The high correlation between predicted values by the models and measured data indicated that the developed models were able to predict the changes of qualitative characteristics of pomegranate arils during storage at different temperatures. Finally, the optimizing of the packaging and storage conditions was done by the genetic algorithm. The major objective of optimization in this study was increasing the shelf life of packaged pomegranate arils by changing the storage temperature, concentration of essential oil and number of perforations on the package. The results showed that shelf life could be increase by lower temperature and higher concentration of Zataria multiflora boiss essential oil. Keywords: Modeling, Modified Atmosphere Packaging, Optimization, Pomegranate aril, Zataria multiflora boiss .