The intestine is a complex multifunctional organ. In addition to digesting and absorbing feedstuffs, the intestine is critical for water and electrolyte balance, endocrine regulation of digestion and metabolism, and immunity. The intestines of carnivorous fish have evolved for processing a highly digestible, nutrient dense diet that is high in protein and low in carbohydrate. Correspondingly, abilities to digest protein are well developed, but carbohydrate digestion is low compared to omnivorous and herbivorous fish. Furthermore, the evolutionary stable diet is associated with a lack or reduced abilities to adaptively modulate digestive functions to match changes in diet composition. Despite similar selective pressures, intestinal structure is highly variable among carnivorous fish, reflecting phylogenetic diversity. Due to economic considerations, diets for cultured species often have varying proportions of plant-based ingredients. Although such feeds are effective for raising omnivorous and herbivorous species, they have provided limited success for carnivores, and this has been attributed to digestive limitations. Recent evidence of inflammatory responses to as yet unidentified components of some plants suggest involvement of the enteric immune system. Changes in temperature and salinity alter intestinal structure and functions, and therefore processing of dietary inputs. A relatively unknown component of the intestine involves the resident microbiota and its role in the health and disease of carnivoraus fish.