Excessive nitrogen input caused by eutrophication in nearshore waters is a major environmental stressor driving the global degradation of seagrass beds. Objective To screen and identify efficient aerobic denitrifying bacteria from seagrass bed ecosystems and elucidate their nitrogen removal performance and mechanisms, thus providing microbial resources for alleviating nitrogen loading and restoring eutrophic seagrass beds. Methods Aerobic denitrifying bacteria were isolated and screened from seagrass rhizosphere sediments in Zhifu Bay, Yantai by enrichment-domestication culture and bromothymol blue assay. The taxonomic status of the strains was determined by 16S rRNA gene sequencing. On the basis of nitrogen removal performance, an efficient aerobic denitrifying strain was selected. Single-factor and orthogonal experiments were conducted to optimize its denitrification conditions, and nitrogen balance experiments and whole-genome sequencing were employed to elucidate its nitrogen removal pathways and key functional genes. Results A total of 34 denitrifying strains were isolated from seagrass rhizosphere sediments in Zhifu Bay, Yantai. The dominant genera were Pseudomonas and Acinetobacter. A strain designated as Pseudomonas sp. S22 with high denitrification performance was selected. The denitrification conditions of this strain were optimized as follows: sodium succinate as the carbon source, C/N=15, pH 9.0, salinity (S)=30‰, and T=28 ℃. Under these conditions, the strain achieved a removal rate of 99.99% for 140 mg/L nitrate nitrogen within 36 h, demonstrating excellent nitrogen removal efficiency. Nitrogen balance analysis revealed that approximately 59.64% of the initial nitrate nitrogen was converted to gaseous nitrogen, confirming that denitrification was the dominant nitrogen removal pathway. Genomic sequencing revealed that strain S22 carried key functional genes for aerobic denitrification, including napA and nirS, providing a genetic basis for its denitrification phenotype at the molecular level. Conclusion This study systematically isolated and identified aerobic denitrifying bacteria from seagrass beds in northern China. Strain S22 exhibits outstanding nitrogen removal performance and environmental adaptability. Nitrogen balance and genomic analyses confirm that denitrification is its primary nitrogen removal pathway and the strain carries key functional genes for aerobic denitrification. Strain S22 can serve as a potential microbial resource for reducing nitrogen loading in seagrass beds. This study provides both a valuable strain and a theoretical basis for the future development of microbe-seagrass synergistic remediation technologies.