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Membrane fouling results in flux decline or transmembrane pressure drop increase during membrane bioreactor (MBR) operation. Physical and chemical cleanings are essential to keep an MBR operating at an appropriate membrane flux. Considerable residual membrane permeability loss that cannot be removed by conventional cleaning requires membrane replacement. This study demonstrates that an internal biofilm can develop inside a hollow-fiber membrane and can probably account for up to 58.9 and 81.3% of total membrane resistance for aerobic granular MBR operated in sequencing batch reactor (SBR) mode or continuous-fed mode, respectively. The Arthrobacter sp. (accession no. AM900505 in GenBank) corresponded to internal biofilm development by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis and the agar-plating technique. This study also identifies a single strain, Arthrobacter sp., generates the internal biofilm. The Arthrobacter sp. is a rod-shaped bacterium with a size close to that of membrane pores, and can secrete excess bound proteins, hence can penetrate and attach itself inside the membrane and grow. Internal biofilm growth could contribute significantly to membrane resistance during long-term MBR operation.