Abstract: Based on the technology of Illumina MiSeq high throughput sequencing, we analyzed the effects of periodic hypoxia stress on intestinal microflora structure of Lateolabrax maculatus, so as to provide references for the study of the adaptation mechanism of intestinal flora of the juveniles to environmental hypoxia. The results show that hypoxia caused a significant increase in the diversity and richness of intestinal microflora (P<0.05). The species richness was rather different between the two groups. The operational taxonomic units (OTUs) of hypoxic group were significantly more than those of normoxic group (P<0.05). At the level of Class classification, the dominant bacteria of both groups were Proteobacteria, Firmicutes and Bacteroidetes. Compared with the normoxic group, the relative abundance of Proteobacteria decreased significantly in hypoxic group, while that of Bacteroidetes increased significantly (P<0.05). At the level of Genus classification, the relative abundance of Alphaproteobacteria and Bacilli in hypoxic group decreased significantly, while those of Clostridia, Gammaproteobacteria and Bacteroidia increased significantly (P<0.05). Periodic hypoxia stress also led to an increase of relative abundance of anaerobes or facultative anaerobes (Anaerolineaceae, Lachnospiraceae and Ruminococcaceae) and oxygen-producing bacteria (Chlorobiaceae) in the intestine of L. maculatus.