The microbiota are normally involved in numerous factors concerned with the health of the fishes in their environment and many of them can also cause threats to the same. In fish, the gut microbiota inhabiting the gastrointestinal tract influence the physiology, nutrition, life span, immunity, besides acting as a barrier against pathogens. Although gut microbiotas are present in all the fish, their composition varies based on their life stages, the environment in which they live, diet, seasons, trophic levels, etc. There are numerous studies related to the intestinal microbiota of freshwater, marine fish and in various life stages of fish. But the knowledge on the microbiota in aquatic ecosystem is yet to be explored. Researches in this field will pave way to the develop techniques to manipulate the gut microbiota of the desired fish species of culture to improve their growth and production. This review is intended to provide collective information on the gut microbiota in fish, their development, dynamics in the living environment and their manipulation towards improving production and sustainability in the field of fisheries.