Aaptos sp., one of marine sponges that can be found abundantly in Indonesian waters, has been reported to produce bioactive metabolite against tumor, pathogenic microbes, and Herpes Simplex Virus type I (HSV-1) (Coutinho et al. 2002). It was detected that the compounds produced were alkaloids, e.g aaptamin, aaptosin and isoaaptamine; the latter compound showed potent activity against Human Immunodeficiency Virus type I (HIV-1) (Gul et al. 2006). Aaptos sp. was also been reported to produce sterol compounds (Rachmat and Muniarsih 2001), and other novel aaptamine alkaloids possesing various biological activities, including cytotoxic against murine lymphoma L5178Y cell line, antiviral, antimicrobial, antifungal, antiparasitic, α-adrenergic antagonistic, radical scavenging, and antifouling activity (Pham et al. 2013).Sponge such as Aaptos sp. is very rich in microorganism including bacteria associated within their body. About 40 % of sponge body is bacteria, and its role is very significant in the sponge metabolism (Taylor et al. 2007). The sponge produces similar metabolites from their associated bacteria (Radjasa et Aaptos sp. is a marine sponge that could produce bioactive compounds such as aaptamin, aaptosin, and isoaaptamin which have activities as antitumor, antimicrobial, and antiviral. Community of bacteria associated with the sponge might correlate with production of those bioactive compounds and be affected by water environment where the sponge grow. The presence of anthropogenic stressor such as pollutans might become a burden to the waters where the biota grown and could affect the microbial biodiversity in the sponge and its active metabolite produced. The objective of this research was to analyze bacterial community associated with Aaptos sp. from Rote Island and Seribu Islands, using T-RFLP method. The results showed that bacterial community associated with Aaptos sp. from both sampling sites shared 40.81% similarity in which they were dominated by the same bacteria class of Actinobacteria, Flavobacteria, α-proteobacteria, δ-proteobacteria, and γ-proteobacteria. The bacteria collected from Rote island were more highly distributed and diverse than those from Seribu Islands. A total of 23 classes of microorganism were identified in Rote Island waters, while in Seribu Islands was 14 classes of microorganism. The presence of Actinobacteria and Proteobacteria in Aaptos sp., is allegedly involved in the production of secondary metabolites.