In aquaculture (shrimp, mollusk, and fish farming), particularly in intensive systems, infectious diseases are always a hazard and can cause significant stock losses and problems with animal welfare. Increasing occurrence of bacterial and fungal diseases whose treatment requires the intensive use of antimicrobials have become common. Even though the aquaculture industry has changed its practices dramatically in order to reduce the use of antimicrobial agents, these agents have contributed and are still important for the advancement of aquaculture. In this chapter, we addressed the main antimicrobial agents used to treat bacterial and fungal diseases in aquaculture. In addition, antimicrobial resistance, a subject of concern not just for clinical microbiologists, but for the whole human population, is also discussed.