Abstract: The 16S rDNA genes of bacteria were amplified and 16S rDNA clone libraries were constructed based on the total DNA extracted from the intestine of and water and sediments in culture ponds of sea cucumberApostichopusjaponicusfrom Yellow Sea and Bohai in spring. The results showed that the bacteria in the intestine and culture pond were composed of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Firmicutes, with dominant Proteobacteria (>41%)in the intestine and culture ponds. Among the four subphyla of Proteobacteria(Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Deltaproteobacteria), Alphaproteobacteria was dominant in the library of seawater in sea cucmber culture ponds from Yellow Sea in spring, while Gammaproteobacteria was dominant group in others.