| Water quality deterioration in aquaculture ponds is a serious problem, and various commercial microbe preparations have emerged, but they have not effectively improved water quality. This study addresses the problem, using directional separation, screening, and propagation of beneficial indigenous bacteria with the objective of improving bio-restoration, purification and remediation of aquaculture wastewater. This approach has the advantages of beneficial effect, high safety, low cost, extended activity and no secondary pollution. In this study, one native denitrifying bacteria, named YJ-1, was isolated and screened from pond water during the mid-late stage (September) of the 2016 aquaculture season. The pond was located in the Yellow River tidal flat of Yuncheng City, the main fish production area of Shanxi Province. During denitrification capacity testing, ammonia was determined with Nessler reagent (yellow) and nitrite was determined with Gries reagent (red). After 24 h of fermentation, ammonia was at a low concentration and nitrite was produced, indicating denitrification. The results of 16S rDNA amplification and sequencing indicated a fragment length of 1441bp. Unrooted phylogenetic tree analysis showed that YJ-1 and Klebsiella oxytoca had the highest homology. Successful isolation of YJ-1 interrupts the trend of microbe preparations coming from commercial sources. If native denitrifying bacteria were added to preparations, ammonia and nitrite nitrogen in aquaculture water could be effectively reduced. Denitrifying bacteria show good potential for application in aquaculture wastewater purification and urban sewage treatment. This study also provides a promising method for isolation, screening, identification and application of other beneficial native bacteria.