The clear relationship between the microbiome and the general well-being of metazoans has motivated the characterization of bacterial communities in cultured species for future microbiome monitoring and modulation to improve productivity. To study the bacterial diversity associated with farmed adult P. monodon at harvest, guts, gastric mills (GM), pond water and sediments were investigated using next-generation sequencing technology in two control ponds (CP1 and CP2) where animals showed a healthy appearance, and two low productive ponds (LP1 and LP2) where animals showed signs of disease. Animals from CP2 were on average at least 4 g heavier than animals from other ponds, and the final yield of both CP was more than double that of LP. LP2 showed the lowest diversity indices, which can potentially be attributed to high abundance of Vibrio spp. and warm water conditions (31.6 ± 0.3 °C on average). The structure of the bacterial community in the gut, GM and water samples was different between CP and LP. Vibrio spp. and anaerobic bacteria (e.g. Fusibacter) were enriched in the gastrointestinal tract of animals from LP (LDA ≥4). While Vibrio can potentially act against the host and other members of the bacterial community, Fusibacter might be an indicator of sulfur compounds accumulation in the animal as the hepatopancreas becomes affected by a PirA toxin. Enrichment of Cyanobacteria in the water (LDA = 4.38) and members of Desulfobacteraceae in sediments of LP (5% on average) could be environmental stress indicators in summer conditions. Characterizing bacterial microbiomes in aquaculture is important to detect indicators of health and productivity that can be used as monitoring tools in the animal's gastrointestinal tract and the environment, ultimately enabling a targeted modulation of the bacterial community for improved production. •Control and low productive P. monodon ponds at harvest exhibit different bacterial communities.•Bacterial assemblages in P. monodon gut from control ponds differ from those in low productivity ponds.•Bacterial communities in guts and gastric mills show indicators of decay in productivity.•Bacterial community in the environment is more diverse than in Penaeus monodon's gut.•Indicators of low productivity include enrichment of Vibrio, Propionigenium and Fusibacter in the gut.