In the present study, to isolate and screen a probiotic that degrades nitrite stably and efficiently, we carried out experiments on enrichment, isolation, culture, and identification of a suitable strain. Then, biological characteristics of the identified strain were determined through optimization of fermentation medium, analysis of nitrite degrading effect, and gene cloning of nitrite reductase. The strain was isolated and screened from five mixed water bodies, including aquaculture projects and wastewater treatment plants, and named JY-1. Additionally, the strain JY-1 was identified using 16S rDNA gene sequence analysis and physiological and biochemical characteristics. The results revealed strain JY-1 to be Bacillus gaemokensis. Optimization of fermentation conditions for sporulation of JY-1 strain indicated that the best carbon source for JY-1 was glucose and the best nitrogen source was tryptone. Analysis of the nitrite-degrading effect of JY-1 showed that JY-1 could degrade 0.6 mg/L nitrite in aquaculture water to 0.0 mg/L in 3 h. Moreover, the safety evaluation test suggested that no hemolysis was found, and the high concentration of JY-1 (109 CFU/mL) had no significant effect on the survival of Nile tilapia. Based on the results of experiments of gene cloning of nitrite reductase and the effect of JY-1 on ammonia, nitrite, and total nitrogen in water bodies, it is preliminarily speculated that enzymatic degradation, operated by JY-1, was the pathway through which nitrite was degraded and removed from water. In summary, this study provides an important basis for the preparation of microecological preparations with high efficiency in degrading nitrite.