Abstract: In this study, traditional culture-based techniques and the 16S rDNA sequencing method were used to investigate the microbial community of the intestinal mucosal layer in the intestine of Miichthys miiuy. We find that the culturable bacteria in each part of M.miiuy digestive tract, sorted from most to least in number, are forefut, pylorus, midgut, hindgut, proventriculus, masticatory stomach and oropharyngeal cavity, and the intestinal tract have the largest number of bacteria colonies; the cultivable bacteria are mainly rod-shaped bacterium and gram-negative bacterium. According to molecular identification of 50 typical strains, the bacteria above are affiliated with γ-proteobacteria (52.7%) and β-proteobacteria (36.8%) in Proteobacteria, and Bacillus in Firmicutes (10.5%); uncultured bacterial 16SrDNA library clones are affiliated with γ-proteobacteria, α-proteobacteria and Deferribacteres. Their partial sequences have low similarity to the reported species, which demonstrates that a new strain may be needed to develop in the digestive tract of M.miiuy.