Abstract: To know the bacterial communities structure in Babylonia areolata culture systems and to research and optimize the management pattern of Babylonia areolata culture systems of the pond mulched plastic film and sand in bottom, the bacterial communities in Babylonia areolata culture systems of the subtidal zone and the pond mulched plastic film and sand in bottom were analyzed at molecular level by adopting the denaturing gradient gel electrophoresis (DGGE). The results indicated that the dominant bacterial communities in Babylonia areolata culture systems of the subtidal zone and the pond mulched plastic film and sand in bottom, which were built on the basis of the seawater in East-island of Zhanjiang, included Proteobacteria Chloroflexi, Cyanobacteria and Actinobacteria. The dominant bacterial groups in the above pond culture system were Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Epsilonproteobacteria, Anaerolineae, Cyanobacteria and Actinobacteria. The dominant bacterial communities in the subtidal zone culture system were Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Anaerolineae and Cyanobacteria, and there were less Epsilonproteobacteria and Actinobacteria in the culture system. The higher diversity was detected in the above two culture systems. The results of unweighted pair group method with arithmetic average (UPGMA) showed that the bacterial communities of the sediment samples S1 and S2 in the above two culture systems were a cluster, the similarity of bacterial communities was 54.5% . The bacterial communities of seawater samples S3 and S4 in the above culture systems were a cluster, the similarity of the bacterial communities was 84.0%. The results showed that the microorganism ecological level in the Babylonia areolata culture systems of the pond mulched plastic film and sand in bottom could be similar to the subtidal zone culture systems through changing the pond seawater and monitoring the microbial population.