River pollution from the agriculture industry has become an important cause of unscheduled water disruptions in Malaysia. Thus, rigorous control and treatment of high strength wastewater prior to discharge into the river are needed. This study aims at evaluating the performance of a pilot membrane bioreactor (MBR) for the treatment of palm oil mill effluent (POME). POME was subjected to MBR operating in an aerobic environment for 40 days, followed by 10 days without aeration and water pumping to simulate failure event, and finally resumed to operational condition. Higher proportions of protein (-PN) compared to polysaccharides (-PS) were present in both the mixed liquor and biofilm, indicating that protein was the main constituent of extracellular polymeric substances (EPS). Biological samples from the mixed liquor and biofilm on the membrane surfaces were collected on day 25,50 and 75 to investigate taxonomic distribution of microbial community. High throughput sequencing of the 16S rRNA gene was used to investigate the composition of microbial communities in the MBR. Microbial groups such as the phyla Proteobacteria (19-23%), OD1 (11-15%), Chloroflexi (11-13%) were the dominant members in biofilm under operational condition while OD1 (20%), Proteobacteria (18%) and Planctomycetes (16%) were found to be dominant in biofilm under static and non-operational conditions. The taxonomic profile of the microbial community on day 75 is more similar to that of day 25, compared to day 50, suggesting the capability of the microbial communities to revert to the operational state despite a period of downtime. (C) 2016 Elsevier B.V. All rights reserved.