To investigate the effects of photosynthetic bacteria as additives on water quality, microbial community structure and diversity, a photosynthetic purple non-sulfur bacteria, Rhodopseudamonas palustris, was isolated and used to remove nitrogen in the aquaculture water. The results of water quality showed that the levels of ammonia nitrogen, nitrite nitrogen, total inorganic nitrogen and total nitrogen in the treatment group were significantly lower (p < 0.05) than the nitrogen levels of the controls in an extended range. A 454-pyrosequencing analysis revealed that at the level of phylum, Proteobacteria and Firmicutes were dominant in the control group respectively, compared to the dominance of the phyla Proteobacteria, Bacteroidetes and Actinobacteria in the treatment group. The relative abundance of phyla Bacteroidetes and Actinobacteria in treatment witnessed an increase than that in the control. The results also indicated that the treatment group enjoyed a higher microbial diversity than that of the control group. Based on the oxygen requirement and metabolism, the authors observed that the water supplementation with photosynthetic bacteria could significantly decrease (p < 0.05) the number of nitrite reducer and anaerobic bacteria. Therefore, the results suggested that adding photosynthetic bacteria to water improves the water quality as it changes the microbial community structure.