The microbiota plays a major role in the health and disease in animals, including maintaining health of the gut, promoting development of epithelium cells, resisting the intrusion of pathogenic bacteria, regulating the absorption harvest of energy and metabolism of lipid. It is a great challenge to the fish gut microbiota research due to the complicated factors, such as differences of fish species, feeding habits or survival environment. Based on the previous related researches, the present article first reviewed the gut microbiota composition of different fishes. Also, the effects of different factors on the gut microbiota of fish were reviewed, such as feed component, water chemical factors, fish species, genotype, developmental stages, aquaculture models and strategies of feeding. Finally, some present issues and future research directions about the fish microbiota were presented.