In spite of restricting rules, antibiotics are still used in aquaculture for prevention, especially during critical phases (early stages; metamorphosis; transfer), but also during on-growing. Besides improving husbandry techniques and prophylaxis, which is still possible, alternative methods are now available or in progress. Commercial probiotics for land animals are increasingly used for shrimp and fish farming, though every species or rearing condition should require particular experiments to determine the most suitable microbial preparations and doses. The variability in response to probiotics, and the lack of reliable data hinder the use of such practices in routine, indeed. These commercial preparations contain Lactobacillus, Bacillus, or other bacteria belonging to related genera, or yeast. They are not suitable for bivalve molluscs like scallops, oysters, and clams. Only few marine bacteria have been documented to protect efficiently larval bivalves against infection. However, many problems remain unsolved regarding legal authorization, production, preservation, and retailing of such preparations with gram-negative bacteria. Probiotics may display multiple effects, possibly combining bacterial antagonism to some effects on the host, e.g. stimulating immunity, or growth, though the modes of action are not fully understood. Probiotics are not as efficient as antibiotics in case of bacterial infection, however. Prebiotics like fructo-oligosaccharides (FOS) may also improve animal health, since they favor the establishment of commensal or beneficial gut microbiota. For instance, an experiment showed that FOS could increase growth of turbot fry. A third alternative may come from antimicrobial peptides, which have been described in many organisms. These peptides have wide spectra of action. They can kill gram negative and gram positive bacteria, envelop viruses, yeasts, and moulds. Several peptides were recently discovered in shrimp and oysters, where they are essential elements of innate defense, in the absence of acquired immunity. These molecules could advantageously replace antibiotics, since they are less susceptible to cause resistance in the target microorganisms, due to their direct action on membranes, and to their fast degradability, which avoid the accumulation of residues.