Microbial fuel cell (MFC) technology is a renewable energy source that employs microorganisms as biocatalysts to degrade substrates into electrons and protons, and then transfer the electrons to the anode electrode. Electron transfer rates by microorganisms depend on many factors as well as on their diverse electron transfer mechanisms. The present study compared cytochromes, flavoproteins, electron transfer complexes, redoxins and other extracellular membrane proteins that have direct involvement in electron transfer mechanisms in Escherichia coli str. K-12 MG1655, Rhodopseudomonas pulastris DX-1 and Shewanella oneidensis MR-1. Escherichia coli str. The results showed that K-12 MG1655 had a more diverse range of extracellular proteins for electron transfer mechanisms compared to Rhodopseudomonas pulastris DX-1 and Shewanella oneidensis MR-1. Escherichia coli str. K-12 MG1655 expressed more flavoproteins, redoxin and electron transfer complex related proteins that had direct involvement in electron transfer mechanisms compared to two other bacterial species indicating that it may be able to transfer more electrons when employed in MFC technique. Escherichia coli str. K-12 MG1655 expressed 16 cytochromes, 9 flavoproteins, 6 redoxins, 6 electron transport complexes, 1 hypothetical and 1 oxidoreductase proteins. On the other hand, Rhodopseudomonas pulastris DX-1 and Shewanella oneidensis MR-1 expressed 26 and 35 cytochromes proteins. But these two bacterial species expressed less flavoproteins and redoxin related proteins and they didn’t express any electron transport complexes or hypothetical and oxidoreductase related proteins for electron transfer. STRING and SMART results suggested that the identified proteins transferred electrons either by connecting with other types of identified proteins in the constructed gene network or independently by taking part in oxidation-reduction reaction, metal ion reduction reaction or by their FMN binding activities.