Scallop aquaculture is threatened by Vibrio bacteria-induced larval mortality, needing the development of sustainable pathogen control strategies. This study investigates the potential of host-derived antimicrobial peptides (AMPs) as eco-friendly alternatives for pathogen control in aquaculture. Exploiting the scallop transcriptome, we identified sequences sharing common AMP features and designed a de novo peptide named helixidin, a 40-amino acid peptide with a net charge of +11 and a pI of 11.52. In addition, we designed an analog, N -ter Ap BD Q13R, based on the hydrophobic domain of the scallop big defensin Ap BD, with a glutamine-to-arginine substitution at position 13. N -ter Ap BD Q13R is a 35-residue peptide with a net charge of +4 and a pI of 11.55. The synthetic peptides helixidin and N -ter Ap BD Q13R adopted an alpha-helix secondary structure with an amphiphilic distribution of amino acid residues. Circular dichroism assays confirmed their structural stability across varying pH, osmolarity, and temperature conditions. Moreover, these peptides displayed potent broad-spectrum antibacterial activity, in the case of helixidin causing cell wall and membrane disruption of Gram -positive and Gram -negative bacteria, respectively. On the other hand, N -ter Ap BD Q13R showed a possible penetrating action on bacterial cells, with formation of nanonets-like structures against the scallop pathogen Vibrio bivalvicida VPAP30. Notably, both peptides exhibited selective activities against Vibrio strains isolated from healthy scallop larvae and specific bivalve pathogenic Vibrio , underscoring their potential for targeting host -associated vibrios. Biosafety tests showed that both peptides are harmless to A. purpuratus larvae. In conclusion, helixidin and N -ter Ap BD Q13R represent novel cationic AMPs with different mechanisms of action against host -associated vibrios, offering promising prospects for sustainable pathogen control in scallop aquaculture.