Intestinal microflora play an important role in animal development and health.In order to evaluate the changes of the bacterial communities in fish intestine upon diseases occurrence,the diseased Cynoglossus semilaevis cultured in two indoor farms with ascites and skin ulceration,and healthy fish in the same farming system were studied by using high through sequencing technique in this paper.The results revealed that bacteria species in fish intestine were obviously less than those in environment,only accounting for 14.3%-44.7% of the bacteria species in pellet feed or tank inlet water.After disease occurrence,the bacteria diversity in diseased fish intestine declined markedly,just 45.8% and 64.5% of the bacteria species in healthy fish coming from the same farming system.For further analysis of these microbial communities structure,although more than 60% bacteria species were different between diseased fish and healthy fish,the dominant bacterial communities' structure in these fish intestine had almost no difference.The first ten dominant bacterial strains in each fish sample were basically the same,their total proportion exceeded 80% of the relative bacteria amount in fish intestine.We also found that different disease occurrence had different effects on half-smooth tongue sole intestinal microflora.The microbial community structure in diseased fish intestine with ascites changed distinctly,while the fish with skin ulceration hardly changed.According to the results of this study,the microflora in cultured half-smooth tongue sole intestine was conservative.But not every type of disease can cause this micro-ecosystem structure change.