Biofloc technology (BFT) is an alternative aquaculture practice that involves the manipulation of carbon-nitrogen ratio (C:N) to manage nitrogenous waste through microbial assimilation. This study aimed to determine the composition of the microbial community present in BFT and describe the microbial community’s response to C:N manipulation. The experiment had a complete randomized design with two set-ups (i.e., BFT and control) in triplicates. The experimental unit was a 120-L rectangular tank stocked with 15 mixed-sex tilapia fish, Oreochromis niloticus, with an average weight of 15±3 g. The C:N was adjusted to 16:1 using molasses. Illumina MiSeq sequencing platform was used, and bioinformatics was conducted in R using dada2 and phyloseq package. Seventeen (17) phyla were identified, but only seven were remarkably abundant, namely: Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, and Fusobacteria. Double Principal Coordinates Analysis (DPCoA), Principal Coordinate Analysis (PCoA) of Weighted Unifrac Distance and Canonical Correspondence Analysis (CCoA) revealed an association of Proteobacteria to low ammonia concentration in BFT treatment. On the other hand, phylum Bacteroidetes was clustered towards the control, characterized by high ammonia. Overall, BFT has increased Shannon and Simpson diversity indices compared to the control. Regime change in the microbial community was not easily caused by organic C supplementation because of community robustness to withstand biotic and abiotic disturbances. Controlled laboratory experiment showed that some bacteria species proliferate as a response to C:N manipulation, but established species remained dominant.