Seagrass meadows are vulnerable blue-carbon ecosystems experiencing global decline. Harnessing endophytic microbes for seagrass conservation requires a mechanistic understanding of host-microbe interactions, which remains largely unresolved. In this study, we aimed to reveal the symbiotic traits of endophytes in the below-ground tissues of seagrass Halophila ovalis, which is widely distributed throughout tropical and temperate regions, from the intertidal zone to deep clear water. To achieve this, we integrated year-round field sampling, multi-omics, bioimaging, rate measurements, and biochemical analyses. Overall, this study identified specific functional traits that facilitate the predominance and adaptation of seagrass endophytes. Our findings corroborate below-ground seagrass tissues as hotspots for diverse nitrogen-fixing bacteria, and demonstrate that evolutionary mechanisms, such as genomic nitrogen cost minimization, horizontal gene transfer, and purifying selection, are critical drivers of endophyte adaptation to below-ground seagrass tissues.