Background <p>The emerging foodborne pathogen, <i>Aeromonas hydrophila</i>, co-infects humans and animals, especially fish, threatening aquacultural production and public health. Previously, we found that <i>Scatophagus argus</i>, a widely cultivated fish species with high economic value, exhibited enhanced growth but increased susceptibility to <i>A. hydrophila</i> infection under freshwater conditions compared to seawater conditions. However, the exact mechanisms involved remain unclear.</p> Results <p>Our study demonstrated that the enhanced virulence of <i>A. hydrophila</i> 201416, isolated from <i>S. argus</i>, in response to increasing salinity was associated with altered quorum sensing-related gene expression and regulated behaviors. Results from virulence assays incorporating phenotypic characterization indicated that elevated salinity levels (from 0 to 35‰) significantly hindered <i>Ah</i>201416 infection of <i>S. argus</i>. This trend correlated with increased biofilm mass and swimming motility, yet was inversely related to bacterial growth. RNA-sequencing and quantitative reverse transcriptional PCR analysis confirmed significant upregulation of genes related to flagellar assembly (<i>flgB</i>, <i>flgH</i>, <i>flgC</i>, <i>flgI</i>, <i>flhA</i>, and <i>fliA</i>), bacterial secretion (<i>HlyD</i> and <i>Ahh1</i>), and quorum sensing (<i>AhyR</i>, <i>LuxO</i>, and <i>LuxE</i>) of <i>Ah</i>201416 in response to elevated salinity. These findings suggested that increased salinity not only enhanced the virulence of <i>Ah</i>201416 but also bolstered the resistance of <i>S. argus</i>, thereby mitigating its susceptibility.</p> Conclusions <p>This study provides deeper insights into the microbial risks associated with <i>A. hydrophila</i> in aquacultural production, which is critical to developing effective prevention and control strategies and ensuring a safe seafood supply.</p> Clinical trial number <p>Not applicable.</p>