The chemical composition of the aerial and root essential oils, hydrodistilled from Artemisia absinthium L. and Artemisia vulgaris L. (wild-growing populations from Serbia), were studied by gas chromatography, gas chromatography-mass spectrometry, and 13C nuclear magnetic resonance. During the storage of plant material under controlled conditions, a significant decrease of essential oil yields (isolated directly after drying and after 1 year of storage) and significant differences in their chemical compositions were observed. A possible mechanism for the observed oil component interconversion has been discussed. The noticeable differences in the chemical composition of the oils isolated from roots and aerial parts of A. absinthium and A. vulgaris were also correlated with the diverging biosynthetic pathways of volatiles in the respective plant organs. The antimicrobial activities against the common human pathogens of all of the isolated oils were tested according to National Committee on Clinical Laboratory Standards. The oils showed a broad spectrum of antimicrobial activity against the tested strains. Therefore, these oils can be used as flavor and fragrance ingredients.