Sludge from an anoxic tank at the centralized wastewater treatment plant, Nong Khaem, Bangkok, Thailand, was inoculated in an anaerobic sequencing batch reactor (ASBR). The optimal compositions and operating conditions of the stock of autotrophic ammonium oxidizing bacteria medium were determined. The process of oxidizing ammonium with bacteria under anaerobic conditions is often referred to as the Anammox process (NO2- to N2 gas, using NH4+ as the electron donor and NO2- as the electron acceptor). The startup period for the anammox culture took more than three months. With ammonium and nitrite concentration ratios of 1:1.38 and 1:1.6, the nitrogen conversion rate zero order. Fluorescent in situ hybridization (FISH) was used to identify specific autotrophic ammonium oxidizing bacteria (Nitrosomonas spp., Candidatus Brocadia anammoxidans, and Candidatus Kuenenia stuttgartiensis). Results from this work demonstrated a shift in the species of ammonium oxidizing bacteria from Nitrosomonas spp. to Candidati Brocadia anammoxidans and Kuenenia stuttgartiensis, with increased ammonium concentrations from 3 mM to 15 mM. Under NH4+:NO2- ratios of 1:1.38 and 1:1.6 the ammonium oxidizing bacteria were able to remove both ammonium and nitrite simultaneously. The specific nitrogen removal rate of the anammox bacteria (Candidati Brocadia anammoxidans and Kuenenia stuttgartiensis) was significantly higher than that of anaerobic ammonium oxidizing bacteria (Nitrosomonas spp.). Anaerobic ammonium oxidizing bacteria (Candidati Brocadia anammoxidans and Kuenenia stuttgartiensis) are strict anaerobes. [ABSTRACT FROM AUTHOR]