Robust process-tolerant and inhibitor-resistant microbes are recognized as key short-term technological goals for the rapid expansion of cellulosic-ethanol production. Zymomonas mobilis is a promising ethanogenic bacterium due to its productivity, high level of ethanol tolerance and its ability to be genetically manipulated. In a series of studies, we have investigated the effects different inhibitors on Z. mobilis using genetics and systems biology tools to better understand the physiology of the organism and its stress responses. We observed maximum specific growth rates were not dramatically different between aerobic and anaerobic conditions, yet oxygen did affect the physiology of the cells leading to the buildup of metabolic byproducts that ultimately led to greater differences in transcriptomic profiles in stationary phase. In stationary phase cultures, there was only 1.7% of the amount of ethanol present aerobically as there was anaerobically. Similarly, the effect of ethanol on Z. mobilis fermentations was profiled using microarray, proteomics, and metabolomics. We have resequenced the genomes of an acetate tolerant mutant and the wild-type strain using comparative genome sequencing via microarray, next-generation 454-pyrosequencing and Sanger sequencing, which identified a 1.5 kb deletion in the mutant strain and many SNPs in both strains. A locus was identified that conferred acetate tolerance in Z. mobilis through systems biology tools, mutagenesis and complementation experiments. Finally, we have updated the Z. mobilis ZM4 genome annotation using a new annotation pipeline and 454-pyroresequencing, transcriptomics, and proteomics data to facilitate the future Z. mobilis studies. An overview of these studies will be presented.