Marine invertebrates in support of his life's defence of sea predatory use an innate immune mechanism, namely the cellular component hemocytes by secreting the dissolved antimicrobial and cytotoxic substances. It shows that marine invertebrates are potential sources and promising antimicrobial compounds. This research was aimed at determining the antibacterial activity of sea urchin (Diadema setosum) extract against some bacterial isolates and its application to foodstuffs. The gonad and shell of sea urchin extracted by methanol and ethyl acetate and then separated by ultrasound-assisted extraction. Screening of antibacterial compound use gas chromatography-mass spectrometry (GC-MS), and disc diffusion method was followed to determine the antimicrobial activity against Salmonella, Escherichia coli and Staphylococcus aureus. The results of this study showed antibacterial activity against one or more strains. The gonad of sea urchin from methanol extract exhibited significant inhibitory effect and effective against Salmonella, E. coli and S. aureus. Majority of gonad and shell of sea urchin extract showed antibacterial activity against the tested strains. However, gonad of methanol extract was found to be inhibiting microorganisms gram-negative (E. coli) and gram-positive (Salmonella and S. aureus). Gonad extract can be a good source of antibacterial agents.