Gut microbiota has a significant effect on fish health, digestion, nutrient metabolism and disease resistance. The aim of the study is to compare the gut microbiota of Nile tilapia from two different aquaculture systems: Pond and bio floc. Gut samples were done DNA extraction, V3-V4 16s rRNA sequencing and analyzed. In this study, gut microbiota is analyzed and checked how the environmental factors like water quality parameters and rearing conditions affect the microbial community.