The Jebel Chakir discharge area, a sanitary landfill, is nowadays the common way to eliminate municipal waste in Tunis (Tunisia). In this study, we developed an anaerobic membrane bioreactor (AnMBR) process for the treatment of Jebel Chakir landfill leachate (LFL). The theoretical organic loading rate ((OLR)-O-T) in the reactor was gradually increased from 4 g COD/1/d to 10 g COD/1/d. The composition, diversity, and changes in microbial communities were analysed using the polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) fingerprint method during OLR increasing. The positive effect of the AnMBR system to maintain stability of the microbial diversity present at the treatment startup during OLR increasing was demonstrated. High loading rate decreased bacterial diversity, but the archaeal one remained stable. At the optimal OLR (7 g COD/1/d), small-subunit (16S) rDNA clone libraries of Bacteria and Archaea populations were performed. The results show that, within the domain Archaea, all phylotypes were related to the CA11 group and one sequence belonged to cultivate genus, the acetoclastic Methanosaeta. Within the domain Bacteria, rDNA genes were affiliated with six phyla: Bacteroidetes, Firmicutes, Synergistetes, Proteobacteria, unclassified bacteria, and Verrucomicrobia. This study related the performance of the AnMBR treating leachate to the change of microbial communities in order to better understand the process and monitor this anaerobic digestion.