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Membrane biofouling constitutes a great challenge in anaerobic membrane bioreactor (AnMBR). Here, we studied the initial deposition of anaerobes, the first step in biofilm formation, with a consortium isolated from an AnMBR on membranes with different surface properties and under two shear rate conditions without filtration. We found that the cell transfer coefficient, calculated from the initial deposition experiments, was similar under the two shear rates for the hydrophobic membranes, but much higher under low shear rate and much lower under high shear rate, for the hydrophilic membrane. The cell transfer coefficient measured under filtration mode and at a higher shear rate showed a similar trend. The pioneer bacteria and archaea (without filtration) were identified by next-generation sequencing. The results showed that the selective force for the dissimilarity of the pioneer bacterial and archaeal diversity was the shear rate and the membrane surface properties, respectively. However, statistical analyses revealed minor changes in the pioneer bacteria (class level) and archaea (order level) populations under the various conditions. These results shed light on the first step of biofilm formation on the membranes in AnMBRs and emphasize the importance of hydrodynamic shear and membrane surface properties on the initially deposited anaerobes.