Immunoglobulin M (IgM) shows potential as a significant immunological marker in Asian seabass (Lates calcarifer), accentuating the importance of developing specific monoclonal antibodies (mAbs) for immunological studies. In this study, we investigated the antigenicity of the IgM heavy chain (IgMH), particularly the Cμ3 region of IgMH (IgMHCμ3), and synthesized a peptide for anti-IgMHCμ3 mAb production. The synthesized peptide was used to generate a specific mAb in rabbits. The produced mAb demonstrated high specificity and affinity for Asian seabass IgMH, as confirmed through indirect ELISA, Western blot analysis, indirect immunofluorescence assay (IIFAT) and flow cytometry analysis. In addition, an indirect ELISA was developed and optimized to measure anti-Flavobacterium covae and anti-Streptococcus iniae antibody titers in Asian seabass serum. The monoclonal antibody (mAb) was subsequently used to assess the health status of Asian seabass post-vaccination and challenge with these pathogens, demonstrating its potential as a valuable tool for immunological studies and health assessments in Asian seabass. Vaccination and postchallenge fish exhibited a pronounced increase in specific antibodies and total serum IgM and IgM+ cell populations. Thus, this study establishes a foundational platform for using the anti-IgMHCμ3 mAb as an essential tool for evaluating and understanding the immune responses and health status of Asian seabass, especially in the context of bacterial infections and vaccinations, and paves the way for more studies in fish immunology.