Thymus species are important aromatic, medicinal and culinary plants with a significant economic value. This study evaluated for the first time the chemical composition and in vitro bioactivities of the essential oils (EOs) from five Moldavian Thymus species (T. vulgaris, T. × citriodorus, T. calcareus) and cultivars (T. vulgaris ‘Faustini’, T. citriodorus ‘Aureus’). The main compounds in Thymus EOs were: thymol in T. vulgaris and T. calcareus EOs (55.44% and 55.45%, respectively), lavandulol in T. × citriodorus EO (54.27%), and geraniol in T. citriodorus ‘Aureus’ and T. vulgaris ‘Faustini’ EOs (60.31% and 31.45%, respectively). T. vulgaris and T. calcareus EOs showed the most potent antioxidant activities (EC50=0.003 mg/mL in ABTS radical cation scavenging assay) and exhibited significant inhibitory effects against aflatoxin‐producing Aspergillus flavus fungus (MIC=0.25 μL/mL). At doses that provided micromolar concentrations of thymol, T. vulgaris and T. calcareus EOs acted genoprotective at preventive and interventional levels against H2O2‐induced genomic damage in V79 cells, the former being more active (6.21% and 5.52% vs. 25.13% and 7.26% tail DNA in pre‐ and post‐treatment protocols, respectively). The genoprotective effects may be ascribed to antioxidant potential and, possibly, to stimulation of DNA repair processes. The Moldavian Thymus species are valuable resources of bioactive EOs for pharmaceutical and food industries (T. vulgaris, T.calcareus) but also for flavor industry and perfumery (T. × citriodorus, T. citriodorus ‘Aureus’, T. vulgaris ‘Faustini’).