Scarce information exists about microbial communities inhabiting the Indonesian deep sea. This study's objective is to assess the ecological role of existing microbial communities from three sediment samples collected at 100, 115 and 1 457 depths from Arafura deep-sea using Next Generation Sequencing. The results indicated the potential diverse microbial role of biogeochemical cycles in depths more than 1 000m. This initial assessment underlines the need for further investigation of deep-sea microbial communities in the Indonesian marine environment.