The membrane fouling layer in the combined aerobic granular membrane bioreactor (AGMBR) process and the conventional MBR process was probed in this study using the multiple staining and confocal laser scanning microscope (CLSM) technique. The fouling layer built up outside and inside the membrane was principally composed of live cells embedded in a matrix of proteins and polysaccharides. The fouling layer presented outside the membrane is noted denser in structure than that inside the membrane.