Probiotics are live microbial feed supplements which beneficially affect the host by improving its intestinal balance. Due to the presence of different bacterial species in the gut of the fish body, the bacterial species are the strong candidates of probiotics in the fish health. This study aimed to characterize the gut micro- biota of Asian stinging catfish (Heteropneustes fossilis) and Nile tilapia (Oreochromis niloticus) treated through biofloc technology. The microbial community from the gut of four individuals from each fish species was identified using 16S rRNA pyrosequencing. The gut microbial community differed significantly between fish species in terms of bacterial species diverseness. However, after the analysis of the gut from the fish body, the micro biome environment were dominated by the phylum Fusobacteria, specifically the species Cetobacterium somerae. The overwhelming dominance of the genus Cetobacterium in all species permits further investigation into its role in the fish gut micro-biota. This study provides the first characterization of the gut micro-biota of two economically significant fishes and establishes a baseline for future probiotic trials under biofloc system in India.