Denitrifying activity of most typical denitrifiers is usually completely suppressed when anaerobiosis is insufficient, aerobic denitrifying bacteria has a major advantage in reducing nitrate and/or nitrite to N2 under aerobic conditions, which is critical for nitrite and nitrate removal from aerobic environment, such as aquaculture water. Aims: To isolate aerobic denitrifying bacteria to enhance nitrate and nitrite removal from aquaculture system. Methods and Results: Selective enrichment culture method under alternating oxic-anoxic conditions was used for screening bacteria that have high capability of aerobic denitrification from a shrimp pond. A novel denitrifier X0412 was isolated and purified after 2 months of incubation. It, identified as Stenotrophomonas maltophilia (formerly referred to as Xanthomonas maltophilia) based on its biochemical and morphological characters, is grouped into the γ subclass of the class Proteobacteria. Phylogenetic analysis of 16S rDNA sequences indicated that strain X0412 was most closely related to S. maltophilia AB021406. Analysis of the both nitrite reductase genes nirS and nirK showed that it contained nirS gene, which is highly homologous to nirS of Pseudomonas stutzeri (formerly referred to as Alcaligenes faecalis A15). When bacterial concentrations as represented by OD600 increased from 0.044 to 0.436, the bacterium reduced the concentrations of nitrite rapidly from 26.18 mgL－1 to an undetectable level within 10 h, with DO titer decreasing from 5.21 mgL－1 to 3.80 mgL－1. Similar result was observed within 20 h at the salinity less than 25‰ . Conclusions: Stenotrophomonas maltophilia strain X0412 reduced nitrite rapidly and efficiently at a high DO concentration and across a wide range of salinity. Significance and Impact of the study: Strain X0412 is highly promising for future potential application in the control of nitrite and nitrate concentration of aquaculture systems.