The structure of microbial communities in a biofloc Technology (BFT) system has a great influence on the optimal functioning of the system. This makes understanding the microbial composition in BFT of paramount importance. A study was conducted to characterise the microorganisms in an indoor biofloc technology system. The microorganisms were qualitatively and biochemically analysed. Qualitative analysis of microorganisms in BFT was carried out using microscopy and plate culture of bacteria and fungi. Isolated bacteria were identified by colony morphology, gram staining, and microscopic observation. Catalase test, as a biochemical test, was also used to identify bacteria. Biochemical analysis of the biofloc was achieved through proximate analysis of nutrients following AOAC (2002) methods. The biofloc sample used in the present study was obtained from culture water of three 1000l circular fiberglass tanks with a working volume of 580l of biofloc water per tank. Oreochromis karongae fingerlings were stocked in the three tanks at a stocking density of 6kg/m3 per tank and cultured for 12 weeks. The fish were fed 30% CP on-farm formulated feed (2mm pelleted) with a feeding rate of 1.5% of the total estimated fish biomass. Maize flour was added in tanks to maintain an optimum C/N ratio (above 10) for heterotrophic bacteria production. Microscopy of the biofloc water revealed various types of microorganisms, which included Protozoa (e.g. ciliates), Zooplanktons (e.g. Rotifers and copepods) and nematodes, heterotrophic bacteria and fungi. It was noted that the bacteria were all heterotrophic, confirming their utilisation of organic carbon in the BFT system to produce microbial protein. The biochemical composition of biofloc showed that the nutritional quality of biofloc was appropriate for tilapia with the exception of lipid content, which was found to be 3.25%. This value is considered low for aquaculture feed as a range of 5- 10% lipid content in feed is recommended. BFT is a promising field, which will enable aquaculture to grow towards an environmentally friendly approach because of the ability of microorganisms to recycle nutrients in the system.