This study investigated the effect of organic carbon source on ammonia oxidizing community in single sludge laboratory scale sequencing batch reactors (SBR). Two sequencing batch reactors performing simultaneous carbon oxidation and nitrification were operated. Operationally and functionally, these two reactors were identical, except that one reactor was fed peptone and sodium acetate, and the other was fed glucose and sodium acetate as external organic carbon sources. The peptone-fed reactor had 98.1 + or – 1.84% COD removal and 97.3 + or – 6.69% NH(3)-N oxidation. The glucose-fed reactor had 99.1 + or – 1.29% COD removal and 99.4 + or – 0.76% NH(3)-N oxidation. The reactor fed with peptone, a complex organic carbon source comprised of enzymatic digests of animal proteins, had greater diversity in both the heterotrophic bacterial community and the ammonia oxidizing bacteria community than in the reactor fed with glucose, a simple sugar as evidenced by automated ribosomal intergenic spacer analysis (ARISA) and terminal restriction fragment length polymorphism (TRFLP) experiments respectively.