Aquaculture is a pivotal sector in global food production, yet it faces significant challenges from disease outbreaks, often exacerbated by the ineffectiveness of antibiotic treatments due to biofilm formation and the emergence of resistant bacterial strains. Marine ecosystems, however, harbour a plethora of unique microorganisms capable of producing bioactive compounds with immense potential as alternatives to conventional antibiotics. These bioactive agents, derived from marine bacteria and fungi, exhibit remarkable properties such as bactericidal activity, surfactant-mediated biofilm disruption, anti-adhesive effects, and quorum-sensing inhibition. Additionally, biomass and biomolecules associated with marine microorganisms are gaining prominence as feed supplements, probiotics, and immunostimulants to enhance the health, growth, and survival of aquaculture species while improving water quality. Marine microalgae, in particular, have emerged as sustainable substitutes for fish oil and fish meal, contributing to environmentally friendly aquaculture practices without compromising nutritional quality. This chapter explores the diverse applications of marine microorganisms in aquaculture, emphasizing their role in disease management and sustainability. By leveraging these natural resources, the aquaculture industry can adopt innovative strategies to mitigate bacterial infections and foster sustainable fisheries for the future.