| Aaptos sp. is a marine sponge which is distributed widely in Indonesia. Aaptos sp. Could produce aaptamin, aaptosin, and isoaaptamin that have activities such as antitumor, antimicrobial, and antiviral. Those metabolite compounds might be produced because of the presence of associated bacteria in the sponge. Analysis of bacterial community associated with Aaptos sp. was done with TRFLP method. The analysis of TRF patterns showed that the bacterial communities on Batu Termanu (Rote Island) and Pejaliran Barat Islands (Thousand Island) were dominated with Actinobacteria, a-proteobacteria, Bacilli, Bacteroidia, Deinococci, d-proteobacteria, and ?–proteobacteria. A total of 23 classes of microorganism were identified in Batu Termanu Island and 14 classes of microorganism were identified in Pejaliran Barat Island with the similarity of bacterial community from Aaptos sp. In the two locations is 40.81%. According to the calculation of diversity index, the microorganisms in Batu Termanu Island were more highly distributed and diverse than Pejaliran Barat Island. The differences of the bacterial community might be caused by phosphate contamination and environmental condition on physical and chemical factors. The presence of Actinobacteria and Proteobacteria in Aaptos sp., were allegedly involved in the production of secondary metabolites. |