| Indonesia which has a wide sea area is a potential country to explore. One of the important research is identification and analysis of genetic diversity on microbial community. Utilization of this research including for data collection on microbial diversity in the regions of Indonesia, bioremediation, bioindicator, the discovery of new drugs, and the discovery of new compounds that have a unique character. The seawater sample was obtained from Pelangi Island, Kepulauan Seribu and Batu Termanu, Rote Island, Nusa Tenggara Timur and assayed with TRFLP. The Terminal Restriction Fragment (TRF) showed that Pelangi Island had 16 classes that dominated by Actinobacteria and Bacilli classes meanwhile Batu Termanu had 7 classes that mainly dominated by Alphaproteobacteria class. The Shannon’s and Simpson’s diversity indexes showed that microbial community in Pelangi Island is more diverse than Batu Termanu. |