An aerobic denitrifying bacterium H2 was selected from the pond sludge by using a new screening method: Samples were enriched by intermittent aeration firstly, secondly limiting diluted, then screened with BTB screening culture medium. Strain H2 was identified as Bacillus sp. according to its physiological and biochemical characters, as well as 16S rDNA sequence homology comparison. The highest degradation velocity of NO3- and NO2- were 0.46 mg/L×d and 0.885 mg/L×d, and the degradation rate of total nitrogen was 45.2% in aquarium water during the 15-day experiment. The study showed that strain H2 had great potential in the biodenitrification of aquaculture.