In order to explore the effect of hypersaline aniline-containing pharmaceutical wastewater on the structure of activated sludge-derived bacterial community, RAPD-PCR and PCR-DGGE techniques were used to analyze the change of bacterial community diversity and structure during the acclimation to different concentrations of two types of wastewater. Different bacterial community structures and significant shift in the bacterial community diversity were observed during the acclimation of wastewater. The number of bacterial species and the abundance of bacteria acclimated to different concentration of wastewater decreased when the concentration increased. The trends of bacterial community diversity indices revealed by RAPD or DGGE profiles were different. The change of bacterial community diversity might be due to the adaptation and mutation under selection issues in the acclimation of wastewater. The relationship between diversity indices and the content of chemical oxygen demand (COD), chloride, salinity and aniline based on RAPD and DGGE data indicated that the change of the bacterial community diversity might not be due to a single factor but might be due to the integrated effects of all the contaminants in the wastewater. Phylogenic trees based on RAPD and DGGE fingerprints were different, indicating that the effect of wastewaters A and B on the bacterial community structure was different, which might be due to the characteristics of wastewater. (C) 2009 Elsevier B.V. All rights reserved.