The gut microbiota plays an important role in host health and disease. Our understanding of the fish microbiota lags far behind our knowledge of that of humans and other mammals. Nevertheless, research has highlighted the importance of the microbiota in the health, performance, and various physiological functions of fish. The microbiota has been studied in various fish species, including model animals, economic fish, and wild fish species. The composition of the fish microbiota depends on host selection, diet, and environmental factors. The intestinal microbiota affects the nutritional metabolism, immunity, and disease resistance of the fish host, while the host regulates the intestinal microbiota in a reciprocal way through both immune and non-immune factors. Improved and novel gnotobiotic fish models have been developed, which are important for the mechanistic study of host-microbiota interactions in fish. In this review, we discuss recent progress in fish microbiota research. We describe various aspects of this research, including both studies on fish microbiota variations and fundamental research extending our knowledge of host–microbiota interaction in fish. Perspectives on how fish microbiota research may benefit fish health and industrial sustainability are also discussed.