An anaerobic moving bed membrane bioreactor (AnMBMBR) fed with synthetic domestic wastewater was investigated under hydraulic retention time (HRT) shocks to assess the effects on the microbial (bacteria and archaea) community and reactor performance. 16S rDNA targeted polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach was optimized to relate the metabolic and community composition with biogas generation, methane content and COD removal efficiency. From the drastic decrease of HRT (from 8 h to 4 h), the methane production was significantly reduced due to the HRT shock, while the COD removal efficiency was not affected. The enhanced growth of homoacetogenic bacteria, Thermoanaerobacteraceae competes with methanogens under shock period. When the HRT was recovered to 8 h, the methane generation rate was higher than the initial operation before the shock HRT changes, which would be ascribed to the activity of new emerging hydrogenotrophic archaea, Methanocella sp. and Methanofollis sp. (C) 2015 Elsevier Ltd. All rights reserved.