With rapidly declining numbers of wildlife fish stocks, the economic importance of aquacultures is on the rise. To optimize production procedure, researchers started to explore the cultured animals gut microbiota, which heavily influences the overall health and nutrient uptake of its host. Here we investigated the microbial communities of the gut content of milkfish from open-cage mariculture in Bolinao, Philippines. We visited 4 fish cages at which fish were collected at two sampling timepoints during the course of a month. Additionally, physiological (body condition index, stress levels) and environmental parameters (oxygen concentration, salinity) were recorded, and the fish feed used at the time of sampling was analyzed for its CN content and microbial community composition. The data submitted here is therefore associated with 2 publications: one about fish physiology and one about microbial community composition. Furthermore, the sampling took place as part of a larger sampling campaign within the ACUTE project (AquaCUlture practice in Tropical coastal Ecosystems- Understanding ecological and socio-economic consequences funding: Leibniz SAW-2015-ZMT-4), during which also sediment and water column microbial communities and environmental parameters were surveyed (sediment: doi: 10.1093/femsec/fiz006, SRA Accession: SRP155505, 10.1594/PANGAEA.900758 water column: ongoing). To investigate the gut microbial community, DNA was extracted from the content of the distal 10cm of the fish gut as well as from 0.5g of fish feed samples using bead beating and Phenol-Chloroform-Isoamylalcohol extraction. Sequencing was conducted at LGC Genomics GmbH (Berlin, Germany). Bash and R scripts for sequence processing, as well as the final OTU table are included in this data submission.