The chemical composition of the essential oils obtained from the leaves and bracts of hydroponically cultivated Origanum dictamnus were analyzed by GC-MS techniques. Three different concentrations of phosphorus (5, 30, and 60 mg/L) in the nutrient solution were used for the cultivation, using the nutrient film technique (NFT). A total of 46 different compounds were identified and significant differences (qualitative and quantitative) were observed between the samples. Carvacrol and p-cymene were identified as the main compounds in all samples analyzed, whereas thymoquinone was found in higher percentage in the leaves than in bracts. The essential oils were tested for their antibacterial activity against Gram-positive and Gram-negative bacteria. The oils obtained from the bracts were found to be more active. The results obtained from GC-MS analyses were submitted to chemometric analysis.