The impact of the two adaptation-induced mutations in an improved xylose-fermenting Zymomonas mobilis strain was investigated. The chromosomal mutation at the xylose reductase gene was critical to xylose metabolism by reducing xylitol formation. Together with the plasmid-borne mutation impacting xylose isomerase activity, these two mutations accounted for 80 % of the improvement achieved by adaptation. To generate a strain fermenting xylose in the presence of high acetic acid concentrations, we transferred the two mutations to an acetic acid-tolerant strain. The resulting strain fermented glucose + xylose (each at 5 % w/v) with 1 % (w/v) acetic acid at pH 5.8 to completion with an ethanol yield of 93.4 %, outperforming other reported strains. This work demonstrated the power of applying molecular understanding in strain improvement.