The predominant bacterial community structure of Dysidea avara and Craniella australiensis in the South China Sea were revealed by PCR- DGGE fingerprinting in the present study. With further cloning, sequencing and phylogenetic analysis, it was found that Proteobacteria predominated in these two sponges. Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria were found in Dysidea avara and only Gammaproteobacteria found in Craniella australiensis. Although Bacteroidetes were found in both sponges, they differed in the species. These bacteria were found in sponges firstly. The bacteria in Craniella australiensis show more complex diversity than that in Dysidea avara. Because compared with Dysidea avara, Craniella australiensis include Actinobacteria, Firmicutes, etc. The bacterial community diversity in these two sponges indicates that the sponge-associated bacteria are host-specific even if the hosts are from the same marine location. DGGE fingerprint-based analysis should integrate with band cloning and sequencing, phylogenetic analysis, etc., molecular techniques to get precise results for the microbial community and diversity revelation. The research of studying sponge microbe by DGGE technique is initial work, that will accelerate the development of sponge microorganisms item.