Presently, there is significant research focused on the use of probiotics and prebiotics in fish and shellfish. These applications have shown various benefits, including improved health, growth performance, feed utilization, disease resistance, gastric morphology, enzyme activities, carcass composition, larval survival, and gene expression. Moreover, prebiotics and probiotics have the potential to mitigate stress responses, reduce malformations, and regulate blood cholesterol levels in aquatic animals. The book highlights the potential advantages of stimulating the inherent immune system, both locally and systemically. Several aquaculture production species, such as European sea bass, Salmonids, gilthead sea bream, African catfish, channel catfish, carp, tilapia, and shrimp, have demonstrated enhanced disease resistance against relevant pathogens, likely due to microbial modulation. This book explores the gut microbiota of aquatic creatures, studying methods and potential uses of probiotics and prebiotics in aquaculture. Controlling gut content significantly impacts the health, growth, and quality of farmed fish and crustaceans. The book covers the science behind using probiotics and prebiotics to improve overall well-being, growth rates, and feed utilization. It is a valuable resource for academics, researchers, and aquaculture specialists, providing insights into gut microbiota and its importance for fish health and performance.