Submerged and external anaerobic dynamic membrane bioreactors (AnDMBRs) have been compared in terms of removal efficiency, filtration characteristics and microbial community structure. High COD removal efficiencies were obtained with both submerged and external AnDMBRs. To obtain an effective dynamic membrane (DM) layer enabling high quality permeate, longer time was required in the external AnDMBR configuration compared to the submerged one. A difference in microbial community structure was identified using pyrosequencing analyses between the submerged and external AnDMBRs. The number of archaeal types decreased in the bulk sludge of the external AnDMBR. External sludge recirculation might have had a negative effect on the archaeal community in the bulk sludge of the external AnDMBR. However, the sludge recirculation in the external AnDMBR configuration led to a filtration at lower total filtration resistance and TMP in comparison to the submerged one at the same gas sparging rate. Results showed that the submerged AnDMBR system can provide a shorter start-up period, slightly better permeate quality in terms of COD concentration, and higher biogas production in comparison to the external one in gas-lift mode.