Some species of marine sponges inhabiting the Ryukyu Archipelago in the Western Pacific are considered to be potential sources for useful natural products, since a number of bioactive compounds have been reported from their extracts to date. In the present study, to understand the basic structure of microbial consortia in marine sponges, which may involve in the production of these chemicals, bacterial communities of eight species of potentially useful sponges were evaluated by pyrosequencing of 16S rRNA gene amplicons. As the results of community analysis using more than 48,000 sequence reads, 9,473 operational taxonomic units (OTUs) were counted from sponge specimens and surrounding sediments, however, in which only a small number of sequences (1.8 %) was shared between sponges and sediments. Fifty-five out of 74 dominated OTUs in sponge specimens were closely related to sponge-derived sequences, which implicated their sponge-dependent life style. It was also evidenced that bacterial communities of Axinella sp. collected from geographically distinct sampling sites (> 400 km) were significantly related each other both in phylum-level composition and in the commonness of some prominent OTUs indicating the universality of stable relationships between marine sponges and their bacterial associates. In addition, the evaluation by fluorescence in situ hybridization (FISH) using nucleotide probes designed for conspicuous rRNA sequences successfully visualized certain dominated cyanobacterial and actinobacterial residents to be distributed over sponge mesophyl. The study presented here extends the census of sponge-associated bacterial communities to potentially useful sponge species that have never been examined and could provide a fundamental information for deeper understanding of the sponge-microbe complex.