Microbes can be promising catalysts for the conversion of chemical energy to electrical energy in important technologies such as bioelectrochemical systems (BESs) that can support biosensing and wastewater treatment applications. The reliability of BESs depends on the ability of microbes to move electrons from various donor substrates to solid phase electron acceptors through a process known as extracellular electron transfer (EET). Although some of the genes responsible for EET have been identified in a few model prokaryotes, we lack system-wide knowledge about how key genetic interactions evolve under BES conditions and how evolution may affect the long-term operation of these systems. Because mutation and evolution together represent an inevitable aspect of any technology that uses engineered or natural strains as biocatalysts, we need to understand how the genome-wide mutational landscape changes over time under various environmental conditions in BESs. We combined the power of experimental evolution and next generation sequencing to identify the rates as well as patterns of single nucleotide polymorphisms in pure cultures of electrogenic bacteria grown under controlled laboratory conditions with or without BES stimuli. Our analysis reveals how genetic makeup of the biofilm vs. planktonic populations of electrogenic microbes diverges away from each other during evolution. Our approach also allows us to reveal previously hidden players in the genetic networks underlying the EET activity during BES operation. Lastly, our results emphasize the need to characterize evolutionary trajectories of potential biocatalysts in pure cultures as well as multi-species communities to advance the development and efficacy of bioelectrochemical systems.