In this chapter, we focus on microbial fuel cells (MFCs) that convert the energy from organic matters into electrical energy using microorganisms. MFCs are greatly expected to be used as a relatively low-cost and safe device for generating renewable energy using waste biomass as a raw material. At present, however, it has not reached the desired practical application because of the low-power generation; hence, improvements on fuel cell efficiency, such as electrode materials, are still being examined. Here, we focus on the microorganisms that can be used as catalysts and play a central role in improving the efficiency of the fuel cells. Several kinds of microbial catalysts are used in MFCs. For example, Shewanella oneidensis has been well studied, and as known, since S. oneidensis transports the electrons generated within the cell to the surface layer, it does not require a mediator to pass the electrons from the cells to the electrode. Furthermore, Escherichia coli and Saccharomyces cerevisiae, a model organism for MFCs, are also used. The improvements of such microbial catalysts have also been proceeding actively. Here, we elaborated on the principle of MFCs as well as the current situation and latest research on the catalyst development.