In bioelectrochemical systems (BES), the catalytic activity of anaerobic microorganisms generates electrons at the anode which can be used, for example, for the production of electricity or chemical compounds. BES can be used for various purposes, including wastewater treatment, production of electricity, fuels and chemicals, biosensors, bioremediation, and desalination. Electrochemically active microorganisms are widely present in the environment and they can be found, in sediment, soil, compost, wastewaters and their treatment plants. Exoelectrogens are microorganisms capable of donating electrons to anode electrode or accepting electrons from cathode electrode and are mainly responsible for current generation or use in BES. However, current generation from fermentable substrates often requires the presence of electrochemically inactive microorganisms that break down complex substrates into metabolites which can be further utilized by exoelectrogens. The growth and electron transfer efficiency of anaerobes depend on several parameters, such as system architecture, electrode material and porosity, electrode potential and external resistance, pH, temperature, substrate concentration, organic loading rate, and ionic strength. In this chapter, the principles and microbiology of bioelectrochemical systems as well as selective factors for exoelectrogens are reviewed. The anaerobic microorganisms and their electron transfer mechanisms at the anode and cathode are described and future aspects are briefly discussed.