The objective of this review is to control fish bacterial diseases or infections through application of some promising novel biocontrol methods, such as probiotics, bio-encapsulated vaccines, and phage therapy, to avoid the disadvantages of traditional one that potentially affects fish and human health. Bacterial infection in intensive fish farming causes mass mortalities and the treatment of that requires the intensive use of chemicals and antibiotics. Several methods have been tried to control fish diseases including the use of antibiotics, but their haphazard use is associated with potentially negative effects as drug resistance and drug residues. The use of probiotics as biocontrol agents for aquaculture is increasing with the demand for environmental beneficial, eco-friendly alternatives for sustainable aquaculture production. The benefits of such supplements include improved food value, inhibition of pathogenic microorganisms, and increased immune response. The bio-encapsulated vaccine appears to be the most attractive method for releasing of vaccines. Several bioactive molecules which are specific for some diseases have been successfully encapsulated with nanoparticles in order to enhance their availability, bioactivity, and controlled delivery. Recently, “reverse vaccine” by using bio-informatics that aids in designing vaccines against infectious pathogens that are difficult to design, especially the intracellular bacteria. Additionally, the use of bacteriophages for biological control of pathogens in cultured fish has gained much interest. Several bacteriophages have been isolated specific to various pathogenic bacteria. Oral administration of phage cocktail is the most suitable way of application in fish, especially when large number of infected fish should be manipulated. Hence, in the following paragraphs, we will discuss some promising novel biocontrol methods that target the fish pathogens like probiotics, bio-encapsulated vaccines, and phage therapy.