Origanum compactum Benth. is considered a highly threatened species due to its overexploitation by local inhabitants. The selection of the most active species, for later cultivation and domestication, is one of the best solutions to save this Moroccan endemic medicinal plant. The aim of this study was to determine the chemical composition of O. compactum essential oils harvested from fourteen sites geographically different within six areas in Northern Morocco and to study their antibacterial activity against four bacterial strains. EOs were isolated using steam distillation and the chemical composition was determined by GC–MS. The antibacterial activity was tested against four bacterial strains (Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Listeria innocua) using the well diffusion assay, then the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) were determined by the micro-dilution method. The results showed that the EOs tested presented a wide variation in the chemical composition, noticed mainly by phenols (21.41 to 69.53% in Melloussa and Ben Karrich, respectively), sesquiterpenes (0.41 to 2.49% in Mharech and Fifi, respectively) and monoterpenes (27.58 to 73.98% in Ben Karrich and Melloussa, respectively). The major components were: carvacrol (2.18–63.65%), p-cymene (6.69–42.64%), thymol (0.16–34.29%) and γ-terpinene (2.95–22.97%). The EOs of O. compactum from the studied sites expressed a significant antibacterial activity against the four strains studied. The diameters of the inhibitory zones varied from 10.33 to 49.00mm, while the MIC values ranged from 0.06 to 0.25% (v/v) and the MBC values varied from 0.12 to 0.5% (v/v).