Abstract: Based on high throughput sequencing technology MiSeq, we analyzed the structure of intestinal bacterial colonies of Apostichopus japonicus cultured in Suspension cage of Fujian. The results show that the units of classification operation (OTUs) of the three samples were 124, 116 and 78, respectively. The abundance of species and dominant strains were rather different among these samples. The maximum of flora′s species abundance was 2.38 in foregut, followed by 2.22 in midgut and 1.24 in hindgut. The hindgut dominant bacteria was Formosa (87.3 8%) and Lactococcus (7.74%), while the dominance of foregut and midgut were Lactococcus and Bacillus. In addition, the percentages of Lactococcus in foregut and midgut were 59.68% and 11.8%, respectively, while the percentages of Bacillus were 62.45% and 12.07%, respectively. In respect of repeatability, the intestinal bacteria found in hindgut also existed in foregut and midgut, and foregut and midgut had six and four unique flora, respectively.