Three heterotrophic nitrifying bacterial strains, HLf01, HBf01and HHf01, were isolated from a pond where genetically improved farmed tilapia (GIFT) (Oreochromis niloticus) was intensively cultured during the annual peak breeding period. Analysis of biochemical, morphological characteristics and sequences analysis of 16S rDNA identified strains HLf01 and HBf01 as Pseudomonas sp., and strain HHf01 as Acinetobacter baumannii. Further analysis of heterotrophic nitrifying medium inorganic nitrogen used showed that most of the ammonia nitrogen was removed after 48 h. Strains HBf01and HHf01 removed 67.9% and 76.7% of the total ammonia nitrogen after 24 h, recording the mass ratio of carbon to nitrogen used as 10.6 to 1 and 11.7 to 1, respectively. Strain HLf01 used a C:N ratio of 22.7 to 1 with a total of 43.8% ammonia nitrogen removed. In denitrifying media, strains HBf01 and HHf01 may have used nitrate and nitrite as the sole nitrogen source by strain HLf01. Generally, all the three strains used nitrogen in the order ammonia > nitrite > nitrate when all the three nitrogen forms were recorded present. Although the bacterial strains consumed dissolved organic carbon, it was limited when ammonia was the main source of nitrogen compared with other forms of inorganic nitrogen. Also, the test of the three strains on aquaculture water showed similar results of efficiency of ammonia nitrogen removal with the test of inorganic nitrogen use. (C) 2014, The Society for Biotechnology, Japan. All rights reserved.