The high potency of tropical marine microorganisms as a source of biologically active compounds is one of the reasons why the researchers still concern to investigate it. Indonesian sponge was known as a very potential producing active secondary metabolite. Several publications have reported that some sponge associate microorganisms contribute to producing active compounds derived from sponge. The purpose of this study was investigating the active antibacterial compounds derived from sponge (Theonella sp) associate microorganisms. Cultivation and characterization of the potent bacterial, extraction, purification and structural determination of antibacterial substance were conducted. Screening of antibacterial activity to the isolated bacterial strain showed that one of the strains M1Sp1.12102015.103b.3 very strongly inhibits Vibrio eltor and Staphylococcus aureus. Separation of ethyl acetate extract using open column chromatography resulted in three potent active antibacterial compounds. Identification of one of the potential active fraction using GC-MS showed that there is Pyrrolidino [1, 2-a] piperazine-3,6-dione compound. Bacterial characterization using 16S-rDNA compared with the NCBI database showed 99.87 % similarity with Bacillus subtilis subsp. Inaquorum.