Escherichia coli has several elaborate sensing mechanisms for response to the availability of oxygen and the presence of other electron acceptors. The adaptive responses are coordinated by a group of global regulators, which include the one-component Fnr protein, and the two-component Arc system. To quantitate the contribution of Arc and FNR dependent regulation under microaerobic conditions, the gene expression pattern of the fnr the arcA and arcB regulator genes, and the glycolysis related genes in a wild-type E. coli, an arcA mutant, an fnr mutant, and a double arcA, fnr mutant, in glucose limited cultures and different oxygen concentrations was studied in chemostat cultures at steady state using QRT-PCR. It was found that ArcA has a negative effect on fnr expression under microaerobic conditions. Moreover, the expression levels of the FNR regulated genes, yfiD and frdA, were higher in cultures of the arcA mutant strain compared to the wild-type. These imply that a higher level of the FNR regulator is in the activated form in cultures of the arcA mutant strain compared to the wild-type during the transition from aerobic to microanaerobic growth. The results also show that the highest expression level of aceE, pflB, and adhE were obtained in cultures of the arcA mutant strain under microaerobic growth while higher levels of ldhA expression were obtained in cultures of the arcA mutant strain and the arcA, fnr double mutant strain compared to the wild-type and the fnr mutant strain. While the highest expression of adhE and pflB in cultures of the arcA mutant strain can explain the previous report of high ethanol flux and flux through pyruvate formate lyase (PFL) in cultures of this strain, the higher level of ldhA expression was not sufficient to explain the trend in lactate fluxes. The results indicate that lower conversion of pyruvate to acetyl-CoA is the main reason for high fluxes through lactate dehydrogenase (LDH) in cultures of the arcA, fnr double mutant strain.