This paper focuses on the long term operation and testing of three Microbial Fuel Cells (MFC) having three different anode materials: commercial carbon felt (C-FELT), polyaniline-deposited carbon felt (C-PANI) and carbon-coated Berl saddles (C-SADDLES). A mixed consortium from seawater was used as inoculum and acetate was used as substrate. Tests were conducted for four months under 1000Ω external load. The maximum power generation was obtained by C-SADDLES (102mWm(-2)) followed by C-FELT and C-PANI, respectively. A similar trend was obtained with the evaluation of electrical energy produced: C-SADDLES (2222J), C-PANI (2183J) and C-FELT (2114J). However, the performance of C-PANI decreased over time, most evidently due to degradation or deactivation of deposited polyaniline by the microorganisms' activity. These results provide evidence that the three-dimensional structure, C-SADDLES, offers excellent biocompatibility, high specific surface area, high conductivity and most importantly these properties are maintained for a long period of time.