Abstract Aquaculture plays an important role in meeting human demand for animal protein. Disease is a critical factor that restricts the green and healthy development of aquaculture. Intensive aquaculture practices can increase the susceptibility of aquatic animals to pathogens due to environmental stress. Antibiotics are commonly used for disease prevention and control, but their frequent use in aquaculture can increase the risk of antibiotic‐resistant bacteria and resistance gene transmission, posing a threat to the health of aquatic animals and humans. Recent studies have shown that bacteriocins have inhibitory effects on different species of bacteria, fungi and viruses, and can even affect natural resistance structures such as bacterial biofilms, presenting promising prospects as antimicrobial agents. Bacteriocins have potential applications in various fields such as agriculture, food and medicine, but limited research has been conducted on their impact on aquaculture disease prevention and control, and the underlying mechanisms remain to be explored. Therefore, this review aims to summarise the classification, sources, preparation methods, antibacterial activity against multidrug‐resistant bacteria and application of bacteriocins as antimicrobial agents in aquaculture disease prevention and control. In addition, limitations of bacteriocin application in aquaculture and future research directions are also discussed.