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The gut microbiota in fish is a natural immune barrier, which can inhibit the colonization and proliferation of pathogenic microorganisms, so as to protect the fish from diseases. Dongting Lake is a vital fish and aquatic organisms' habitat and gene pool, with more Cypriniformes and Perciformes species present than Siluriformes. The fish community structure and biodiversity in Dongting Lake have attracted extensive attentions, whereas the ecosystem has been damaged to a certain extent. Few studies have taken the characteristics of fish intestinal microbiota as a potential factor to improve the ecosystem of Dongting Lake. In order to detect the microbial community in important fish populations in Dongting Lake. The 16S rRNA high-throughput sequencing was used to characterize the gut bacterial community diversity, composition and potential functions of six fishes including Pelteobagrus fulvidraco, Siniperca chuatsi, Carassius auratus, Culter alburnus, Ctenopharyngodom idella, Hypophthalmichthys molitrix, which are in Siluriformes, Perciformes and Cypriniformes. There were five dominant phyla in all fish gut samples, including Fimicutes, Proteobacteria, Fusobacteriota, Actinobacteriota and Cyanobacteria. The bacterial composition of Cypriniformes and Perciformes was similar. The proportion of Cetobacterium in Siluriformes was high, while the proportion of Cetobacterium and Aeromonas in Cypriniformes were high. The species composition and function of the microbial community of the gut microbiota of the six fish species were predicted. We found that the species richness of the gut microbiota of Siniperca chuatsi was the highest, and the metabolic process was more vigorous. We speculated that this may be related to the disease resistance and adaptability of Perciformes. An in-depth understanding of the diversity, composition and potential functions of fish gut microbiota can not only better regulate the use of probiotics and their water quality management, but also have important reference values for the healthy breeding of fish. [ABSTRACT FROM AUTHOR]