Phage therapy is a promising alternative to antibiotics in aquaculture, which is facing increasing concerns over antimicrobial resistance (AMR). Bacteriophages are viruses that specifically infect and replicate within bacteria, causing bacterial cell death. They are abundant in the aquatic environment and can be isolated from a variety of sources, including fish, water, and sediment. Phage therapy has been shown to be effective against a wide range of bacterial pathogens that are responsible for causing severe disease outbreaks in aquatic fauna. Phages are highly host-specific, and therefore they can target and eliminate harmful bacteria while leaving beneficial ones unaffected. As a targeted therapy, phage therapy can be used in delicate environments like fish hatcheries where the use of broad-spectrum antimicrobials may disturb the microbial equilibrium with adverse effects on the quality of the developing larvae. However, phage therapy in aquaculture and the aquatic environment faces several challenges. The most important challenge is the rapid development of resistance by the bacteria against phage infection. In addition, a big challenge is the lack of knowledge about the diversity and distribution of phages in aquatic environments. As such, identifying and isolating phages that are effective against specific bacterial pathogens can be time-consuming and resource-intensive, especially taking into consideration the strain diversity of several aquatic pathogens like the vibrios. Additionally, the efficacy of phage therapy can be affected by environmental factors, such as temperature and pH, and the presence of other microorganisms in the environment which can influence the host–phage interactions. Moreover, not only the regulatory framework of phage therapy applications but also the manufacturing of phage products is still far from being established. Despite these challenges, the potential benefits of phage therapy in aquaculture are significant. It offers a sustainable and environmentally friendly alternative to antibiotics, which can reduce the risk of AMR and environmental pollution. Moreover, phage therapy can be tailored to specific bacterial pathogens, which can improve treatment efficacy and reduce the risk of non-target effects. Overall, phage therapy has the potential to revolutionize the way bacterial infections are managed in aquaculture, leading to improved health and welfare of farmed aquatic animals and sustainable aquaculture practices.