The chemical composition of pomegranate juice in terms of organic acids, sugars, vitamin C, total phenolics, catechins and anthocynanins from two Macedonian varieties “Karamustafa” and “Hicaz” was first objective of this study. Furthermore, morphological and physical characteristics of pomegranate fruits from autochthonous “Karamustafa” and “Hicaz” variety were compared. The level of the anthocyanins was significantly higher to “Hicaz” pomegranate variety and it was in good correlation to the results of hue and color of the juice. The most statistically significant difference was obtained for ascorbic acid which was four time higher for freshly squeezed juice from “Hicaz” pomegranate variety. In addition, the variation of chemical composition of elements of fruit juices from both variety could be attributed to the difference in cultivar. Finally, the last objective of our study was antibacterial activity of peel extracts from both varieties. The strong antibacterial activity against Staphylococcus aureus (ATCC 25923) was significant without statistical differences between both varieties.