Although flooding can often severely damage crop yields, few studies of this stress have been made at the genetic level. To identify the genes that probably function in plants at the onset of flooding stress, we constructed a cDNA library representing tobacco plants that experienced short-term stress, i.e., 2 to 4 h of submergence while under illumination. Differential screening of that library produced 73 cDNA clones that showed preferential hybridization with the probe prepared from these stressed plants. The cDNA inserts were isolated from the vector by restriction digest and subjected to reverse northern analysis, which confirmed preferential expression of 41 genes. The remainder either had no significant increase in expression under flooding stress or exhibited no identifiable signal. We then performed northern blot analyses for some selected genes to provide supporting evidence that strongly paralleled our results from the reverse-northern evaluation. Photosynthesis-related genes were the major group, followed by those for well-known glycolysis enzymes and fermentation enzymes. Other genes include those for hydrolytic enzymes and components of the ethylene synthesis pathway. Although many others also were induced, their functions could not be characterized here.