A four-compartment periodic anaerobic baffled reactor (PABR) was run in a'clockwise sequential' switching manner continuously fed on chinese traditional medicine industrial wastewater under an alkalinity concentration between 1000 and 1500 mg CaCO3/L of the feed with average organic load rate (OLR) at about 1, 2, 4 and 6 kg COD/(m(3) d) for 12, 24, 24 and 6 d, respectively. Hydraulic residence time was 2d, while switching period was 4d. As the average OLR increased to 6 kg COD/(m(3) d), the time of the sharp fall in pH, chemical oxygen demand (COD) removal, gas production and methane percentage of the biogas of all the compartments and the time of rapid volatile fatty acids accumulation in effluent coincided, hence the PABR became sour. Denaturing gradient gel electrophoresis (DGGE) community fingerprints and their cluster analysis revealed that community structures of each compartment tended to be more closely related if the PABR was not overloaded. (c) 2008 Elsevier Ltd. All rights reserved.