Galectins are a member of the β-galactoside binding protein family, which play a pivotal role in the immune defense of vertebrates as a pattern recognition receptor and occupy an important position in the innate immune system of invertebrates. The study of galectins in aquatic organisms has only recently emerged. Galectins in aquatic animals exhibit agglutination activity toward bacteria, inhibit bacterial growth, and enhance phagocytosis of immune cells. Additionally, some galectins contribute to the antiviral immune defenses of aquatic animals. This review aims to review recent advancements in the antimicrobial mechanisms, molecular structures, and evolution of galectins from fish, mollusks, and crustaceans. The antimicrobial galectins, as crucial components in the innate immune defense, pave new avenues for developing innovative disease control strategies in aquaculture.