In recent years, biofloc technology (BFT) has become an important water-saving and emission-reducing aquaculture model in aquaculture development. However, in high-density farming ponds, the concentrations of ammonia and nitrite are often much higher than established standards. High ammonia and nitrite concentrations are harmful in aquaculture, where they increase the stress experienced by shrimp, resulting in disease outbreaks. The removal of ammonia and nitrite is an effective method of reducing water pollution resulting from residual food and feces. The Y2 strain, which can efficiently remove ammonia and nitrite, was isolated from the culture water of . Experiments investigating the physiology-biochemistry of this strain and the similarity of 16S rRNA gene sequences have been conducted. The safety of Y2 was evaluated by an immersion infection and antimicrobial susceptibility test. The fermentation conditions, including temperature, pH, and salinity, were optimized, and dynamic changes between bacterial growth and the concentration of pollutants in water were investigated. Water quality, the amount of bioflocs, the number of pathogenic bacteria, and the growth and survival rates of shrimps were monitored through a 28-day culture experiment. The Y2 strain was preliminarily identified as , based on physiological and biochemical characteristics and 16S rRNA sequence analysis. The strain was resistant to oxacillin and clindamycin. Optimum fermentation of the Y2 strain was observed under conditions of 30℃, pH 7.0, and 2% salinity. The 48 h half-lethal concentration of the strain to Artemia was higher than that of cfu/mL, and this strain was nontoxic to cultured animals. The Y2 strain continuously removed ammonia and nitrite from aquaculture water. It inhibited the growth of vibrios, increased the survival and growth rates of shrimps, and was able to survive in water for a long period of time. Therefore, the Y2 strain has high potential as a probiotic for aquaculture and may be used as the key bacterium to regulate water quality in bioflocs culture systems.