Bioluminescence means the ability of animals or plants to naturally produce light. The three known ways by which bioluminescence is produced are through specific cells called photocytes, bioluminescent glands in tissues and symbiotic bioluminescent microorganisms. Bioluminescence in Loligo duvaucelii is known to be caused by the presence of symbiotic microorganisms in bioluminescent sacs. There is a need to compile more information on bioluminescent symbiotic microorganisms on marine life in Indonesia and their potential. This study aims to determine the species of bioluminescent microorganisms on squid and fish, namely Loligo sp. and Loligo edulis from the waters of Jepara and the Bombay duck (Harpadon nehereus) from the Strait of Malacca, Indonesia and their potential. The samples were collected by isolating the microorganisms from the luminescent organs, after which the bioluminescent microorganisms were used in the research. This research consisted of antimicrobial tests against pathogenic microorganisms which were conducted qualitatively. The bioluminescent microorganisms were identified using biochemical assay and molecular assay (16S rRNA PCR). Tests results from Loligo sp. symbiotic microorganisms found two isolates which showed antimicrobial activities against pathogenic Multi Drug Resistant (MDR) microorganisms, namely uncultured bacterium clone 1P-1-G05 against Escherichia coli with 32.59 mm of inhibitory zone and Uncultured bacterium clone 3g10a against Enterobacter sp. with 28.44 mm of inhibitory zone. The bioluminescent symbiont microorganisms in Loligo edulis, which was identified to be Photobacterium phosphoreum, showed antimicrobial activities against Vibrio harveyi, E. coli, Staphylococcus aureus, and Bacillus sp. Bioluminescent symbiotic microorganisms on H. nehereus identified Alteromonas macleodii, which showed gamma hemolysis on the blood agar test.