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Seagrass microbiomes can play pivotal roles in the health and nutrition of the host plant, but are subject to disturbance due to environmental changes and exposure to stressors. To examine the resilience of leaf microbiomes we performed mesocosm experiments with Z. marina shoots where plants were exposed to different antibiotics and dosages for 48 hours and then the recovery of the microbial communities was tracked over time. All antitbiotic treatments led to an intital and strong decrease in alpha diversity and significant changes to the community structure of leaf microbiomes as compared to those from unexposed control plants. Following this disturbance, alpha and beta diversity metrics rapidly return to the level of control plants. These findings that antibiotic-induced stress strongly impacts the leaf phyllosphere community of seagrasses, but that the microbiome is resilient to disturbance and rapidly recovers to a non-stressed state within 16 days.