Abstract: For the purpose of exploring the microbial community structure and bacteriostasis mechanism of Fujian cage farming Apostichopus japonicus,diversity of the dominant strains isolated from the intestinal tracts of Apostichopus japonicus was analyzed using 16S rDNA sequence homology comparison method. The bacteriostatic ability of probiotics and their metabolites lipopeptide compounds were determined,and their antibacterial components were preliminarily determined by thin layer chromatography(TLC)..The results showed that 95 strains of dominant bacteria were isolated and purified,which included 31 strains of potential probiotics,37 strains of potential pathogens and 27 strains of common intestinal bacteria. Microbial community structure analysis found that the abundance of Pseudoalteromonas and Acinetobacter genera were higher while that of Bacillus genus was lower in diseased group than those in healthy group. It would be one of the possible causes of the body surface lesion of Fujian Apostichopus japonicus. Taking 8 strains of typical pathogenic strains as indicator bacteria,two probiotic strains with wide antimicrobial spectrum and high bacteriostatic ability were screened out,which were Bacillus amyloliquefaciens YD1 and Bacillus subtilis YK5. Their lipopeptide metabolites had obvious bacteriostatic effect. The bacteriostasis components were preliminarily determined to be cyclic peptides containing hydrophilic components. The study provided an important basis for the development of functional probiotics and novel microecologics.