As two obligatory intermediates of denitrification, both NO and N2O had harmful environmental and biological impacts. An aerobic denitrifying bacterial strain PCN-1 was newly isolated and identified as Pseudomonas stutzeri, which was capable of high efficient nitrogen removal under aerobic condition with maximal NO and N2O accumulation as low as 0.003% and 0.33% of removed NO3(-)-N, respectively. Further experiment taking nitrite as denitrifying substrate indicated similar low NO and N2O emission of 0.006% and 0.29% of reduced NO2(-)-N, respectively. Reverse transcription-polymerase chain reaction (RT-PCR) analysis revealed that the coordinate expression of denitrification gene nirS (for cytochrome cd1 nitrite reductase), cnorB (for NO reductase) and nosZ (for N2O reductase) was the fundamental reason of low NO and N2O accumulation. Activated sludge system bioaugmented by strain PCN-1 demonstrated a significant reduction of NO and N2O emission from wastewater during aerobic denitrification, implied great potential of PCN-1 in practical applications.