The growing negative perception of consumers towards synthetic chemicals has shifted the search for new antimicrobials to those derived from natural sources (e.g., plants). Oregano and thyme are both well-known aromatic plants that belong to the Lamiaceae family. Their essential oils (EOs) have been extensively studied for their bioactivity which is attributed their rich content in secondary metabolites, especially terpenoids such as carvacrol and thymol. In this study, EOs from oregano (Origanum vulgare subsp. hirtum) and thyme (Thymus capitatus) plants organically cultured in Lemnos island (north-eastern Greece) were investigated for their antimicrobial actions against three foodborne pathogenic bacterial species (i.e. Salmonella enterica ser. Typhimurium, Listeria monocytogenes and Yersinia enterocolitica). For this, the minimum inhibitory concentrations (MICs) and minimum biofilm inhibitory concentrations (MBICs) of each EO against the planktonic and biofilm growth, respectively, of each pathogen were determined. To calculate the MICs, the broth microdilution method was used, while before the calculation of MBICs, the optimal conditions for biofilm formation by each target microorganism were determined using 96-well polystyrene microplates as the growth substrata. Results revealed that the MICs ranged from 0.031% to 0.125% (v/v) depending on the EO and the target pathogen, with the thyme EO to be always more potent than that of oregano. The MBIC values of oregano and thyme EOs were the same for S. Typhimurium at 0.125% (v/v), as well as for L. monocytogenes at 0.031% (v/v). On the other hand, to inhibit the biofilm growth of Y. enterocolitica oregano EO need to be applied at 0.063% (v/v), whereas thyme EO at 0.031% (v/v). The results demonstrated that the EOs of two endemic organic plants of a Greek island both present strong antibacterial action and could be further exploited as natural antimicrobials for food and health applications.