The aquaculture sector has recognized antimicrobial resistance (AMR) as a significant challenge in recent years. The increase in antibiotic resistance among farmed fish is a notable concern for the aquaculture industry. Due to the frequent bacterial infections in fish populations, antibiotics must be regularly administered, resulting in their ongoing presence in the aquatic environment. Hence, this condition promotes the quick spread of antibiotic-resistant bacteria. It is apparent that a significant number of disease-causing microorganisms can develop resistance to antimicrobial substances. AMR within aquaculture systems can be transferred to medically important strains in the natural environment through horizontal gene transfer, which has the potential to affect the entire ecosystem. Among cultured fish, including ornamental varieties, a broad spectrum of pathogens displays resistance to multiple antibiotics. A thorough understanding of gene transfer processes such as plasmids, transposons, and gene cassettes is crucial for unraveling the complexities of antimicrobial resistance in the context of aquaculture. The control of AMR dissemination in aquaculture involves the initiation of continuous monitoring initiatives, the rapid detection of resistant bacterial strains, and the enforcement of regulations. This chapter offers an outline of antibiotic use and the presence of AMR genes in emerging multidrug resistant pathogens, as well as the prevalence of infectious diseases. It also provides into antimicrobial use within aquaculture systems and explores the management of pathogen infections in the field of aquaculture.