Recent studies have reported that genotoxicity is increased significantly in wastewater with a high ammonia concentration after chlorination. Thus, this paper studied the effect of ammonia on the formation and speciation of trihalomethanes (THMs) and haloacetic acids (HAAs) during the chlorination of two different biologically-treated wastewater samples from different sources. The formation of THM species was suppressed with increasing ammonia concentration in both samples, but the effect of ammonia concentration on the formation of HAA species (as dichloroacetic, bromochloroacetic, and bromodichloroacetic acid) was quite different. The yields of dihalogenated species occupied the greatest fractions of the total HAAs (over 46%) in both wastewater samples under the experiment scope. However, regarding the distribution of mono-, di-, and trihalogenated species in HAAs, there were discrepancies between the wastewater samples from different sources. The bromine incorporation factors n(Br) and n'(Br), as a function of ammonia concentration, were influenced by the Br(-)/N mass ratio in wastewater chlorination, and were constant when the Br(-)/N mass ratio was lower than 0.003 (or 0.53 microMmM(-1)) due to the low concentrations of bromide ions.