Abstract: Flora on eipthelia of diseased juvenile sea cucumberApostichopusjaponicuswith body length of 3-5 cm showing body wall lesions was studied by a method of 16S rDNA cloning library. The results showed that the bacteria were composed of Alphaproteo bacteria, Betaproteo bacteria and Gammaproteo bacteria, with the predominant flora ofShigellasp.,Acinetobactersp. andPseudomonassp. on the lesions of the diseased sea cucumber as well as sea cucumber without obvious symptom. There was 49% ofShigellasp., 17% ofAcinetobactersp. and 5% ofPseudomonassp. in the diseased sea cucumber, while there was 20% ofShigellasp., 26% ofAcinetobactersp. and 9% ofPseudomonassp. in those without lesions. The members of Alphaproteo bacteria, Betaproteo bacteria and Gammaproteo bacteria were found in the seawater from the culture ponds as a control group, with predominant phaproteobacteria includingVibriosp.(75%) andShigellasp.(12%).Also, a predominant bacterium strain was isolated from the diseased cultured sea cucumber by a traditional method based on bacterial culture, and identified asVibriosp. by 16S rDNA cloning library. The findings indicate that the predominant flora is varied with the identifying method including a traditional method and 16S rDNA cloning library.