The microbial community in minimal-exchange, superintensive culture systems should be managed to cycle nutrients and enhance production. This paper explores the effects of biofloc concentration reduction and a fish-free diet on several microbial community characteristics. In 16, 3.5-m diameter, 71-cm deep outdoor tanks, shrimp were stocked at 460/m3. Eight of the tanks received a fish-free, plant-based feed and eight received a conventional feed containing fishmeal and fish oil. Within each diet type, biofloc concentration was reduced in four of the tanks and was not reduced in the other four tanks. Photosynthetically active radiation (PAR) extinction coefficients, photosynthetic oxygen production, chlorophyll-a (chl-a) concentrations, pheophytin-a (pheo-a) concentrations, and the sum of odd and branched chain fatty acid concentrations as a bacterial abundance indicator (BAI) were measured. Biofloc reduction significantly (P≤ 0.003) decreased PAR extinction coefficients, chl-a concentration, pheo-a concentration, and BAI concentration, while significantly increasing photosynthetic oxygen production. Diet did not significantly affect (P > 0.05) any of these measured parameters. The observed changes in microbial community characteristics corresponded with, and may help to explain, significantly improved shrimp feed conversion ratios, growth rate, final weight, and biomass yield in the tanks with biofloc reduction.