Bioluminescent bacteria (BLB) are the most widely distributed light-emitting microorganisms, most of which are found as symbionts of free-living marine organisms, including the crustacean species. In this study, 4 out of 7 marine crustaceans in the northeastern section of Manila Bay were found to contain bioluminescent bacteria. Marine crustacean species namely Thenus orientalis (Oriental Slipper Lobster), Oratosquilla oratoria (Mantis Shrimp), Penaeus monodon (Giant Tiger Prawn), Litopenaeus vannamei (Whiteleg shrimp), Scylla serrata (Mud Crab), Portunus pelagicus (Blue Swimming Crab), and Charybdis feriata (Crucifix crab), were swabbed after collection. Bioluminescent bacteria were isolated from the inner surface of the carapace, eyes, abdomen, and abdominal segments of the crustacean samples. All glowing colonies were isolated and upscaled. Only bioluminescent bacteria from T. orientalis, O. oratoria, and P. monodon completed the isolation process and were identified using 16S rRNA gene sequencing for phylogenetic analysis. Furthermore, results from molecular identification through Nucleotide BLAST identified that it was Vibrio alginolyticus and Mucus bacterium. At the same time, the presence of Vibrio rumoiensis was also identified which was proved to be understudied and needs exploration. This study was aimed to identify the present bioluminescent bacteria in selected marine crustaceans in Manila Bay, Philippines through microbiological isolation, molecular identification, and phylogenetic reconstruction.