The marine ecosystem was considered a significant receptor site for environmental contamination, particularly with bacteria. Microbiome from Posidonia oceanica leaves collected from the central-eastern of Tunisia (Coastal of Mahdia) was identified using 16S rRNA gene sequencing. Susceptibility to several antimicrobial agents was studied using the microdilution method. Essential oils extracted from three Tunisian plants, Syzygium aromaticum, Juniperus phoenicea, and Cupressus sempervirens, were tested against the identified strains. A microdilution checkboard assay displayed the combination of essential oils and amoxicillin. Staphylococcus arlettae (MN889255.1) and Bacillus sp. (MG591719.1) were isolated from the microbiome of seagrass meadows (Posidonia oceanica) leaves. These isolates were multidrug-resistant bacteria. Essential oils extracted from J. phoenicea exhibited the highest antibacterial activity. Combining this essential oil with amoxicillin showed an important action against Bacillus sp and S. arlettae isolates. These natural products showed promising activity in reating or preventing fish infections to reduce the use of conventional antibiotics in marine ecosystems. EOs could be used to avoid and/or treat fish infectious diseases and could promise a reduction in conventional antibiotics in aquaculture.