Effect of acidic condition on the fermentation characteristics was investigated by the continuous culture of Escherichia coli. In accordance with down-regulation of crp gene transcript level as well as up-regulation of arcA, the expressions of the TCA cycle genes were down-regulated, which caused more acetate formation at acidic condition under aerobic condition. It was also shown that yfiD was up-regulated in accordance with up-regulation of fnr, and the respiratory pathway genes were up-regulated under acidic condition. The effect of phoB gene knockout on fermentation characteristics was also investigated. Under micro-aerobic condition, the fermentation pattern changed in such a way that formate and lactate were more produced at lower pH due to up-regulations of pflA, yfiD and ldhA genes, whereas ethanol was less produced as compared to the case at neutral pH. The overall regulation mechanism under acidic condition was clarified based on fermentation characteristics and gene transcript levels.