Abstract The use of antibiotics for the control of infections has not only been banned by FDA for use in food-producing animals, but also several countries have prohibited their use in aquaculture because of several reasons such as the occurrence of antibiotic-tolerant microorganisms, accumulation of antibiotic residues in fish and shrimp flesh, and aquatic environmental effluence concerns. These issues have led researchers and aquaculture scientists to conduct several studies to find antibiotic alternatives. Numerous substitutes have been evaluated, such as probiotics, synbiotics, prebiotics, postbiotics, phytogenics, essential oils, and several others. Results show that these supplements demonstrate proven efficacy in enhancing immune responses, reducing mortalities resulting from experimental infections, and reducing antibiotic usage in medicated aquafeed. Nonetheless, using antimicrobial peptides (AMPs) to control fish diseases and be used as antibiotic alternatives is a promising and interesting research topic. AMPs are a vital class of small peptides that could stimulate the innate immune system against challenging pathogens and also possess significant potent defensive responses against a variety of infectious and non-infectious pathogenic agents, including bacteria, parasites, fungi, and viruses. Regarding their source origin, AMPs can be classified into six main types: mammalian-, amphibian-, insect-, aquatic-, plant-, and microorganism-derived AMPs. On account of their unique structure, they can display an essential function in therapeutic strategies against infectious diseases affecting fish and shrimp. Reports showed several kinds of AMPs had a wide spectrum of antimicrobial properties. These effects are besides their prominent immunostimulatory functions. Thus, they may be considered a functional alternative to antibiotics in aquaculture. This article provides information on the current knowledge about the modes of action, sources, classification, functions, and potential applications for the development of aquatic animal health. The information included in this context will be valuable to enhance the sustainability of aquaculture.