Aquaculture is one of the fastest-growing food production systems globally. However, diseases are a key constraint to sustainable aquaculture production systems. Certain bacterial pathogens, e.g., Aeromonas, Vibrio, Flavobacterium, and Streptococcus, cause notable economic losses in fish and shellfish farming. Conventional treatments for these diseases include antibiotics. However, their misuse is resulting in antimicrobial resistance, pollution of the environment, and possible hazards to human health. Hence, eco-friendly options for sustainable aquaculture production systems are urgently needed. Bacteriophages are viruses that specifically target and kill bacterial cells. Phage therapy is a method for using bacteriophages for the treatment of bacterial diseases in aquaculture production systems. Phages are viruses that target specific bacterial pathogens while leaving other harmless microbes intact. Several researchers have shown that phage therapy can reduce disease-causing bacteria in aquatic animals and increase their survival rates. Phages are naturally present in aquatic systems and can replicate in infected tissues. Phages are thus an eco-friendly option for sustainable aquaculture production systems. Though bacteriophages have limitations in their use for aquaculture production systems, their use in phage therapy is promising for sustainable aquaculture production system.