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The emergence of new multidrug-resistant (MDR) pathogens brought attention to the need for new antimicrobial compounds. One of the advances in addressing the global issue of antibiotic resistance is the discovery that microorganisms residing inside medicinal plants (i.e., the endophytes) may contribute to the production of metabolites of pharmaceutical interest. In this work, the composition of the essential oil (EO) and the cultivable bacterial communities isolated from three different species belonging to the genus Origanum , i.e., O. vulgare ssp. vulgare, O. vulgare ssp. hirtum and O. heracleoticum were analyzed, to check the possible nexus existing between them. The three species exhibited different EO aroma profiles, revealing two trans -sabinene hydrate chemotypes and a carvacrol chemotype. The composition of the bacterial endophytic cultivable microbiome isolated from flowers, leaves, and stems and the bacterial communities isolated from bulk soil were characterized at the genus, species, and/or strain level. The analyses revealed a high degree of biodiversity and a low number of strains shared between the three plant species and compartments of the same plant, suggesting the existence of one or more forces responsible for the distribution of the endophytes in the different microenvironments of the plant. Data obtained also suggested that the composition of the EO might be involved in the structuring of the microbial community and that bacteria might be able to colonize the plant since they are resistant to the antimicrobial activity exhibited by the EO itself and/or able to utilize some compounds as a carbon and energy source. Lastly, the composition of microbial communities might enhance or influence the EO composition. [Display omitted] • Three Origanum plants exhibited different essential oil aroma profiles. • Cultivable bacterial endophytes were isolated and molecularly characterized. • A very low number of bacterial strains was shared between plants. • Different plant compartments were inhabited by different endophytic communities. • Essential oil composition might be involved in the structuring of the microbiome. [ABSTRACT FROM AUTHOR]