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The present study aimed to analyze the enhancement of innate immune responses in juvenile-stage common carp (<i>Cyprinus carpio</i> L.), upon the administration of heat-killed <i>Aeromonas hydrophila</i> at a dosage of 1 × 10⁷ CFU ml⁻¹ through bio-encapsulation in the aquatic crustacean, <i>Artemia salina</i>. This work emphasizes the modulation of innate immune response when administered with the bio-encapsulated heat-killed antigen that acts as an inactivated vaccine against Motile Aeromonas Septicemia disease. Bio-encapsulated oral administration of antigens promotes innate immunity in juvenile-stage fishes. The optimization of effective bio-encapsulation of bacterin in <i>Artemia salina</i> nauplii was carried out and the best optimal conditions were chosen for immunization. The functional immune parameters such as myeloperoxidase, lysozyme, alkaline phosphatase, antiprotease and respiratory burst activity in serum, blood and intestinal tissue samples were analyzed along with blood differential leukocyte count and tissue histopathology studies. Both humoral and cellular immune responses analyzed were substantially induced or enhanced in the treatment groups in comparison with the control group. The results showed a significant variation in the bio-encapsulation group than the control group and also were comparable to the protection conferred with immersion route immunization under similar conditions. Thus, most of the innate non-specific immune responses are inducible, despite being constitutive of the fish immune system, to exhibit a basal level of protection and a road to better vaccination strategy in <i>Cyprinus carpio</i> L. aquaculture worldwide.