Abstract: The intestinal flora is essential in shaping many of its host's functional attributes .The microbial community structure in gut，including anterior intestine，middle intestine and posterior intestine of sea cucumber （Apostichopus japonicus）， was studied by 16S rDNA sequence analysis. The results showed that 240 strains were identified from A. japonicus in suspension cage closely relating to 3 Phylum， 11 genera and 34 different species. from the cultivated sea cucumbers in suspension cage. Similarly， 211 strains were relating to 3 Phylum， 11 genera and 49 different species from the sea cucumbers in ponds. The structures of flora were quite different between each part of intestinal， and microflora populations of the entire gut and between the sea cucumbers from ponds and suspension cage were quite different. Vibrio， Formosa and Shewanella were predominant flora in the gut of sea cucumber in suspension cage. Vibrio， Bacillus and Halophilous were predominant flora the gut of sea cucumber from in pond. There were 7 bacteria， which not only existed in the intestinal of sea cucumber in ponds but also existed in the gut of sea cucumber from suspension cage. However they dwelled in different parts of intestines. The species abundance in the gut of sea cucumber from ponds was significantly higher than those in suspension cage. The number of Bacillus and other probiotics were also higher．