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Big defensins are two-domain antimicrobial peptides (AMPs) that have highly diversified in mollusks. <i>Cg</i>-BigDefs are expressed by immune cells in the oyster <i>Crassostrea gigas</i>, and their expression is dampened during the Pacific Oyster Mortality Syndrome (POMS), which evolves toward fatal bacteremia. We evaluated whether <i>Cg</i>-BigDefs contribute to the control of oyster-associated microbial communities. Two <i>Cg</i>-BigDefs that are representative of molecular diversity within the peptide family, namely <i>Cg</i>-BigDef1 and <i>Cg</i>-BigDef5, were characterized by gene cloning and synthesized by solid-phase peptide synthesis and native chemical ligation. Synthetic peptides were tested for antibacterial activity against a collection of culturable bacteria belonging to the oyster microbiota, characterized by 16S sequencing and MALDI Biotyping. We first tested the potential of <i>Cg</i>-BigDefs to control the oyster microbiota by injecting synthetic <i>Cg</i>-BigDef1 into oyster tissues and analyzing microbiota dynamics over 24 h by 16S metabarcoding. <i>Cg</i>-BigDef1 induced a significant shift in oyster microbiota β-diversity after 6 h and 24 h, prompting us to investigate antimicrobial activities in vitro against members of the oyster microbiota. Both <i>Cg</i>-BigDef1 and <i>Cg</i>-BigDef5 were active at a high salt concentration (400 mM NaCl) and showed broad spectra of activity against bacteria associated with <i>C. gigas</i> pathologies. Antimicrobial specificity was observed for both molecules at an intra- and inter-genera level. Remarkably, antimicrobial spectra of <i>Cg</i>-BigDef1 and <i>Cg</i>-BigDef5 were complementary, and peptides acted synergistically. Overall, we found that primary sequence diversification of <i>Cg</i>-BigDefs has generated specificity and synergy and extended the spectrum of activity of this peptide family.