To investigate the immune response of zebrafish to iron-related proteins and SWCNT-encapsulated proteins, we overexpressed and purified two iron-related recombinant proteins (A0KLQ6 and A0KH89) from Aeromonas hydrophila. We then vaccinated Danio rerio with these proteins and their SWCNT-encapsulated counterparts via both intraperitoneal injection and immersion immunization, and found they evoked a strong immune response in D. rerio. When challenged with virulent A. hydrophila, D. rerio administered 5 μg intraperitoneal injections of A0KHR9, A0KLQ6, A0KH89, SWCNTs-A0KHR9, SWCNTs-A0KLQ6 and SWCNTs-A0KH89 obtained high relative percent survivals (RPSs) (61.60%, 65.39%, 84.96%, 68.10%, 77.50% and 90.43%, respectively). Meanwhile, the D. rerio administered 40 mg/L immersion immunizations of aboved samples had 30.80%, 25.85%, 37.80%, 63.60%, 73.74% and 68.49% RPSs, respectively. These results indicate that the outer membrane proteins A0KLQ6 and A0KH89 can be used as potenial subunit vaccine candidates against A. hydrophila infection, and the SWCNTs-encapsulated counterparts can significantly improve the immune effect in both immunization ways. Our studies may provide a theoretical basis for the development of vaccines and adjuvants candidates