Microbial fuel cells (MFCs) can generate electricity simultaneously with wastewater treatment. For MFCs to be considered a cost-effective treatment technology, they should quickly re-establish a stable electroactive microbial community in the case of system failure. In order to shorten startup times, temporal studies of anodic biofilm development are required, however, frequent sampling can reduce the functionality of the system due to electroactive biomass loss; therefore, on-line monitoring of the microbial community without interfering with the system’s stability is essential. Although all anodic biofilms were composed of Desulfuromonadaceae, MFCs differed in startup times. Generally, a Desulfuromonadaceae-dominated biofilm was associated with faster startup MFCs. A positive PCR product of a specific 16S rRNA gene PCR primer set for detecting the acetate-oxidizing, Eticyclidine (PCE)-dechlorinating Desulfuromonas group was associated with efficient MFCs in our samples. Therefore, this observation could serve as a biomarker for monitoring the formation of an efficient anodic biofilm. Additionally, we successfully enriched an electroactive consortium from an active anode, also resulting in a positive amplification of the specific primer set. Direct application of this enrichment to a clean MFC anode showed a substantial reduction of startup times from 18 to 3 days.