Abstract: The bacterial communities structures and their correlativity in half-smooth tongue sole (Cynoglossus semilaevis Gnther) digestive tract, pellet feed, pond water, and sediment were analyzed using high-through sequencing technique. The results revealed that bacteria diversity in pellet feed, pond water and sediment were higher than that in fish digestive tract. The microbial community in fish digestive tract had no relevance to the microflora in pond water and sediment, but it was slightly influenced by the microflora in pellet feed. Our findings also showed that the bacteria strain diversity difference existed in different positions of fish digestive tract, and their bacterial communities' structures were not obvious different. These dominant bacterial strains and their relative proportion in different positions of fish digestive tract were very similar. In addition, most dominant bacteria in half-smooth tongue sole digestive tract cannot find the close sequences in NCBI database. These results suggest that microflora in cultured half-smooth tongue sole digestive tract may be a relatively independent microbial ecosystem. This micro-ecosystem was hardly influenced by the bacteria in culture environment. Some bacterial strain's colonizations in this fish digestive may be species-specific.