Cultured finfish are an important source of animal protein worldwide and the Food and Agriculture Organization (FAO) reported that over half of the world's supply of fish and shellfish is now from aquaculture. This chapter provides an overview of the fish immune system and the infectious diseases of fish (bacterial, viral, parasitic, and fungal). It discusses the adaptive immune system of fish which is divided into two branches: cell‐mediated and humoral immunity. Bacterial pathogens are typically identified following isolation in pure culture by growth in or on media, and are characterized using gram‐staining, acid fast‐staining, and biochemical (nutrient) tests. The chapter focuses on emerging or re‐emerging viral diseases affecting fish that are significant or potentially significant for aquaculture species. Maintaining good water quality, minimizing stress, and providing adequate nutrition are major factors impacting the immune system of fish, and ultimately the innate and acquired immune responses to pathogens.