Although aquaculture is a growing productive sector, economic losses because of infectious diseases and public health concern of what antibiotic resistance represents have become factors that limit its development. Thus, the control of infectious diseases through antibacterial alternatives is a field of intense research. In this sense, antimicrobial proteins and peptides might represent a safe and effective alternative because their site of action is on microbial components; they are biodegradable; their diversity in terms of mechanisms of action is broad; and some of them can be highly specific. Because this antibacterial alternative is still in research, this review provides a critical analysis of the challenges and opportunities of protein drugs for the treatment of bacterial diseases in the field of aquaculture health; contextualizes the different types of antibacterial protein and peptides, their mechanisms of action, potential sources, as well as the state of the art on assessment of antibacterial proteins and peptides in bioassays with aquatic organisms; and discusses the challenges proteinaceous drugs face regarding their stability for oral delivery and the perspectives for their administration in aquaculture.

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Shrimp culture is a well‐established and fast‐growing industry that produces economic and social benefits in many countries. However, during the last years, it was severely affected by the emergence of the Early Mortality Syndrome (EMS) or Acute Hepatopancreatic Necrosis Disease (AHPND). This disease is mainly attributed to Vibrio parahaemolyticus, and currently, there is no effective cure or treatment. In this study, the use of T2A2 and VH5e bacteriophages was evaluated to control different AHPND‐positive strains (presumptively identified as V. parahaemolyticus, VPAHPND) under laboratory conditions. Lytic effect of T2A2 and VH5e bacteriophages against different strains isolated from AHPND outbreaks was corroborated. In addition, the effectiveness of the mixture of both phages was tested on a brine shrimp experimental infection model using three highly virulent VPAHPND strains. It has been found that phage‐treated brine shrimp had significantly higher survival percentage compared with non‐treated groups (p < .001). Also, phage cocktail was found to be harmless to the organisms. These results suggest that the phage mixture is worth considering as a possible control measure for positive AHPND strains, although it is clear that further and more extensive testing is needed.