The bacterial community composition in gut contents，including anterior intestine，middle intestine and posterior intestine of sea cucumber （Apostichopus japonicus），was studied by 16S rDNA PCR denaturing gradient gel electrophoresis （PCR-DGGE）. The band numbers in posterior intestine were significantly higher than those in anterior intestine and middle intestine （P = 0.003， P = 0.016，respectively），which showed that the bacterial diversity in posterior intestine was higher than that in anterior intestine and middle intestine. UPMGA cluster analysis revealed that the bacterial community in posterior intestine had higher similarity than that in anterior intestine and middle intestine among different individuals. Phylogenetic analysis of 13 cloned bands showed that bacterial phylotypes were closely related to α-proteobacteria，γ-proteobacteria，δ-proteobacteria，bacteroidetes and mollicutes，and γ -proteobacteria were the dominant bacteria in the three parts of the digestive tract in A. japonicus. The closest relative bacteria of 12 cloned bands in the present study were from marine environment，which suggested that the bacteria in the gut contents of A. japonicus were from the surrounding habitat environment.