Distribution and occurrence of Archaea and methanogenic activity in a laboratory scale, completely mixed anaerobic reactor treating pharmaceutical wastewaters were investigated and associated with reactor performance. The reactor was initially seeded with anaerobic digester sludge from an alcohol distillery wastewater treatment plant and was subjected to a three step feeding strategy. The feeding procedure involved gradual transition from a glucose containing feed to a solvent stripped pharmaceutical wastewater and then raw pharmaceutical wastewater. During the start-up period, over 90 % COD removal efficiency at an organic loading rate (OLR) of 6 kg COD m(-3) d(-1) was achieved with glucose feeding, and acetoclastic methanogenic activity was 336 ml CH4 gTVS(-1) d(-1). At the end of the primary loading, when the feed contained solvent stripped pharmaceutical wastewater at full composition, 71 % soluble COD removal efficiency was obtained and acetoclastic methanogenic activity decreased to half of the rate under glucose feed (166 ml CH4 gTVS(-1) d(-1)). At the end of secondary loading with 60 % (w/v) raw pharmaceutical wastewater, COD removal dropped to zero and acetoclastic methanogenic activity fell to less than 10 ml CH4 gTVS(-1) d(-1). Throughout the course of the experiment, microbial community structure was monitored by DGGE analysis of 16S rRNA gene fragments. Five different archaeal taxa were identified and the predominant archaeal sequences belonged to methanogenic Archaea. Two of these showed greatest sequence identity with Methanobacterium formicicum and Methanosaeta concilii. The types of Archaea present changed little in response to changing feed composition but the relative contribution of different organisms identified in the archaeal DGGE profiles did change. (c) 2005 Elsevier Ltd. All rights reserved.