Pathogens use cell density dependent gene expression known as Quorum Sensing (QS) to launch virulent factors. Targeting the QS circuit without killing the pathogens is a very promising alternative to using antibiotics which generate antibiotic resistance. The identity and diversity of bioluminescent bacteria associated with Philippine aquatic organisms, and their potential as sources of anti-QS or quorum quenching (QQ) molecules remain unknown. In this study, out of 43 organisms, 30 were observed to harbor bioluminescent bacteria with 26 from marine and four from freshwater sources. Purified bioluminescent bacterial cultures were screened for QQ activity using motility assay and the membrane fractions (MF) of 5 isolates from marine organisms namely Johnius sp. (croaker), Sillago sp. (golden-lined sillago), Variola louti (yellow-edged lyretail), Strombus variabilis (variable conch), Cistopus indicus (octopus), and one from a freshwater host, Chanos chanos (milkfish), inhibited the QS-mediated swarming of Pseudomonas aeruginosa strain NSRI based on statistical analysis using Paired t-test and Univariate Analysis of Variance (p < 0.05). Despite the host differences, the bacterial isolates shared evolutionary relationship with commonly known bioluminescent genera based on 16S rRNA gene sequence analysis with five strains belonging to the genus Photobacterium (P. leiognathi and P. mandapamensis, 99-100% identity), and two to the genus Vibrio (V. harveyi and V. campbellii, with 99% identity).