This research aimed to understand the bacterial diversity in the gut of wild Brachymystax lenok and screen extracellular enzyme-producing strains. We analyzed the species diversity of bacteria based on 16S rRNA phylogenetic relationships and screened isolates that produced extracellular enzymes including amylase, protease, cellulase and lipase. A total of 18 bacterial genera isolated were respectively belonged to Proteobacteria, Bacteroidetes and Firmicutes. Aeromonas were the dominant groups. On the basis of culture-independent approach, a total of 22 bacterial genera were classified into Proteobacteria, Bacteroidetes and Firmicutes and Chlorophyta. Sphingomonas were the dominant genera (Table 1, Fig. 3, 4). Screening of enzyme activities showed that 53 strains produced different extracellular enzymatic activities and that 21 strains could produce extracellular enzymes in a low temperature (Table 2). This study revealed that combination of traditional separation culture and modern molecular biotechnology based on 16S rRNA gene cloning could be used to effectively analyze the bacterial diversity in the gut of wild B. lenok from Qinling mountainous regions and to obtain diverse enzyme-producing bacterial strains.