Phospholipid fatty acid (PLFA) profiles in four full-scale activated sludge reactors (ASR14) treating municipal wastewater, South Korea, were monitored to evaluate the influence of influent water quality on microbial community structure (MCS) and the effect of the MCS on effluent water quality. In ASR13, PLFA profiles were very similar, regardless of the influent water quality and seasonal differences, and 16:17c/15:0iso2OH and 16:0 were dominant. PLFA profiles in ASR4 during summer and autumn were very similar to those in ASR13, but increases in specific fatty acids, 16:1 omega 5c, 11methyl18:1 omega 7c and 15:0iso3OH, were found in ASR4 during winter and spring, with relatively high total suspended solid (TSS) concentrations in the effluent. 16:1 omega 5c and 15:0iso3OH, possibly related with Flexibacter sp., caused a bulking problem in the activated sludge. The community diversity indices such as Shannon diversity and equability decreased in summer but increased in autumn in all the ASRs. Canonical correspondence analysis results suggested that the influent BOD concentration played the most important role in changing MCS, followed by influent TSS concentration. In addition, the TSS and total phosphorus concentrations in the effluent were significantly affected by the change of the MCS.