Thymus capitatus and Thymus broussonnetii are two Moroccan endemic medicinal plants used traditionally by the local population. The present study aims to investigate their essential oil chemical composition, antioxidant and antibacterial activities. The chemical composition of the essential oils was determined using the GC-MS analysis, the antioxidant activity assessed using DPPH and FRAP methods while the antimicrobial activity was evaluated against nine bacteria species tested (Enterococcus faecalis, Serratia fonticola, Acinetobacter baumannii, Klebsiella oxytoca, sensitive Klebsiella pneumoniae, sensitive Escherichia coli, resistant Escherichia coli, resistant Staphylococcus aureus and Enterobacter aerogenes). The major identified compounds of T. capitatus essential oil where carvacrol (75%) and p-cymene (10.58%) while carvacrol (60.79%), thymol (12.9%), p-cymene (6.21%) and γ-terpinene (4.47%) are the main compounds in T. broussonnetii essential oil. The bioactivity of the essential oils of the two species of thyme was explained by their richness in oxygenated monoterpenes known for their great effectiveness with an IC50 of 3.48 ± 0.05 and 4.88 ± 0.04 μL/mL and EC50 of 0.12 ± 0.01 and 0.20 ± 0.02 μL/mL in the DPPH and FRAP assays, respectively, with an important antibacterial activity. These results encourage the use of these plants as a source of natural antioxidants, and antibacterial additives, to protect food from oxidative damage and to eliminate bacteria that are responsible for nosocomial infections