Marine sponges are hosts of diverse bacteria that live in both intracellular and intercellular spaces of the multicellular animals. The aim of this study is to investigate the bacteria diversity inside the marine sponge cells of Hymeniacidon perleve by 16S rDNA gene sequences. To obtain pure sponge cells, a protocol has been developed in which the sponge tissues were firstly dissociated in CMFSW and cleaned several times. The purified sponge cells were subject to extraction of endocelluar bacterial DNA. The endocellular bacterial phylogenetic diversity of the marine sponge was determined by RFLP-16S rDNA sequencing of cloned DNA fragments. Thirteen of isolated 16S rDNA gene sequences were attributed to be alpha-Proteobacteria (5), gamma- Proteobacteria (5) and Planctomycetes (3). When compared to the bacterial diversity of the sponge tissues, alpha- and beta-proteobacteria are still the dominant bacteria genes, however Planctomycetes was not obtained in the sponge tissuse. These results indicated a different bacterial diversity in the sponge cells and sponge tissues.