Acute hepatopancreatic necrosis disease (AHPND) is caused by PirAB toxin-producing Vibrio parahaemolyticus and has devastated the global shrimp aquaculture industry. One approach for preventing the growth of AHPND-producing Vibrio spp. is through the application of beneficial bacteria capable of inhibiting these pathogens. In this study, we focused on the inhibitory activity of Bacillus inaquosorum strain T1, which hinders V. parahaemolyticus growth in coculture experiments in a density-dependent manner; inhibition was also observed using cell-free supernatants from T1 stationary-phase cultures. Using mariner-based transposon mutagenesis, 17 mutants having a complete or partial loss of inhibitory activity were identified. Of those displaying a total loss of activity, 13 had insertions within a 42.6-kb DNA region comprising 15 genes whose deduced products were homologous to nonribosomal polypeptide synthetases (NRPSs), polyketide synthases (PKSs), and related activities, which were mapped as one transcriptional unit. Mutants with partial activity contained insertions in spo0A and oppA, indicating stationary-phase control. The levels of expression of NRPS and PKS lacZ transcriptional fusions were negligible during growth and were the highest during early stationary phase. Inactivation of sigH resulted in a loss of inhibitor activity, indicating a role for σH in transcription. Disruption of abrB resulted in NRPS and PKS gene overexpression during growth as well as enhanced growth inhibition. Our characterization of the expression and control of an NRPS-PKS gene cluster in B. inaquosorum T1 provides an understanding of the factors involved in inhibitor production, enabling this strain's development for use as a tool against AHPND-causing Vibrio pathogens in shrimp aquaculture.IMPORTANCE The shrimp aquaculture industry has been significantly impacted by acute hepatopancreatic necrosis disease (AHPND), resulting in significant financial losses annually. AHPND is caused by strains of the bacterial pathogen Vibrio parahaemolyticus, and treatment of AHPND involves the use of antibiotics, which leads to a rise in the number of antibiotic-resistant strains. Alternative treatments include the application of beneficial microorganisms having inhibitory activities against pathogens causing AHPND. In this study, we examined the ability of Bacillus inaquosorum strain T1 to inhibit the growth of an AHPND-causing Vibrio strain, and we show that this activity involves a gene cluster associated with antibacterial compound production. We found that gene expression is under stationary-phase control and that enhanced activity occurs upon inactivation of a global transition state regulator. Our approach for understanding the factors involved in producing B. inaquosorum strain T1 inhibitory activity will allow for the development of this strain as a tool for AHPND prevention and treatment.