Aeromonas salmonicida (A. salmonicida) is a pathogenic bacterium that causes furunculosis and poses a significant global risk, particularly in economic activities such as Atlantic salmon (Salmo salar) farming. In a previous study, we identified proteins that are significantly upregulated in kidneys of Atlantic salmon challenged with A. salmonicida. Phosphoproteomic analyses were conducted to further clarify the dynamic changes in protein phosphorylation patterns triggered by bacterial infection. To our knowledge, this is the first study to characterize phosphorylation events in proteins from A. salmonicida-infected Atlantic salmon. Overall, we identified over 5635 phosphorylation sites in 3112 proteins, and 1502 up-regulated and 77 down-regulated proteins quantified as a 1.5-fold or greater change relative to control levels. Based on the combined data from proteomic and motif analyses, we hypothesize that five prospective novel kinases (VRK3, GAK, HCK, PKCδ and RSK6) with common functions in inflammatory processes and cellular pathways to regulate apoptosis and the cytoskeleton could serve as potential biomarkers against bacterial propagation in fish. Data from STRING-based functional network analyses indicate that fga is the most central protein. Our collective findings provide new insights into protein phosphorylation patterns, which may serve as effective indicators of A. salmonicida infection in Atlantic salmon.