Symbiont bacteria are microbes that live in a mutualistic relationship with their hosts, produce secondary metabolites such as adenine riboside, polycarpaurine which act as bioactive compounds. This study aims to isolate and analysis bioactive compounds of symbiont bacterial isolates form Polycarpa aurata based on different pH and sea depths in Barrang Lompo Island, Makassar city as antibacterial. 34 isolates of symbiont bacteria coloured-blue Polycarpa aurata is a active isolate were isolated based on pH variation and sea depths. The result of isolate at pH 6 with sea depth 5 and 15 meters = 4 isolate, 5 isolates at sea depth 10 meters, pH 7 with sea depth 5 metes = 4 isolates, 3 isolates at sea depth 10 and 15 metes, pH 8 with sea depth 5 and 15 metes = 4 isolates at and 3 isolate at sea depth 10 meters. Antagonist test of 17 isolates as pure isolate, obtained 13 pure isolate inhibition against 10 pathogenic bacterial. Growth optimization revealed that the optimal growth times symbiont bacteria isolates, namely AQB10-1, AQB10-2 isolate = 22 hours, AQB10-3 isolate = 34 hours and AQB10-5 isolate = 32 hours with the nutritions used in AQB10-1 and AQB10-2 isolate is yeast extract, AQB10-3 is meat, and AQB10-5 isolate is triptone. Molecular analysis was performed through 16S rRNA sequencing, identified as Bacillus licheniformis strain (AQB10-1, AQB10-2, AQB10-3 isolate), Paenibacillus alvei strain (AQB10-5 isolate) and Pseudomonas aeruginosa strain (ALB10-5). Antibacterial activity of symbiont bacteria isolates Polycarpa aurata, obtained the largest inhibition zone diameter in AQB10-2 isolate against Vibrio cholerae ATCC 25175. The bioactive compounds of AQB10-2 isolate containing 1,4-dimethyl-, butanoic acid, azulena, 3-Methyl-2,3,6,7,8,8a-hexahydropyrrolo[1,2-a]pyrazine-1,4-dione, cyclo(L-prolyl-L-valine), hexadecanoic acid, cis-13-Octadecenoic acid, lycopersen, dodec-11-enylbenzene, and 1,2-Benzenedicarboxylic acid compound.