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Pathogenic <i>Aeromonas</i> spp. are the etiological agents of Motile Aeromonas Septicemia (MAS). This study aimed to identify the pathogen of diseased tadpoles (<i>Quasipaa spinosa</i>) and the antibiotic-resistance characteristics of this bacterium. A Gram-negative bacterium, named strain QST31, was isolated from the ascites of diseased tadpoles and was identified as <i>Aeromonas media</i> based on physiological and biochemical tests, as well as molecular identification. Artificial infection experiments showed that strain QST31 was highly virulent to tadpoles, with an LC₅₀ of 2.56 × 10⁷ CFU/mL. The antimicrobial susceptibility of strain QST31 was evaluated using the disk diffusion method, and the results indicated that strain QST31 was resistant to 28 antibacterial agents. In addition, the whole genome of strain QST31 was sequenced, and the presence of antimicrobial resistance genes, integron, and transposon was investigated. Genes involved in adherence, hemolysis, type II secretion system (T2SS), T6SS, iron uptake system, and quorum sensing were identified in the genome of strain QST31. More than 12 antimicrobial resistance genes were predicted in the genome of strain QST31. Interestingly, a novel Tn<i>7709</i> transposon harboring <i>sul1</i>, <i>aadA16</i>, <i>catB3</i>, <i>bla</i>_OXA-21, <i>aac</i>(6′)-IIa, and <i>tet</i>(A) genes was identified. In conclusion, this is the first report on the isolation and identification of pathogenic <i>A. media</i> with multidrug resistance genes from diseased tadpoles. The results revealed that preventing and controlling aquatic animal diseases caused by multidrug resistance <i>A. media</i> will be a huge challenge in the future.