Physiological and molecular adaptation mechanisms enable plants to improve their survival under harsh conditions, including low oxygen levels caused by flooding. When Arabidopsis was exposed to hypoxia, we observed hyponastic response, shoot elongation, leaf chlorosis, and inhibited growth. To understand this response, we used a specialized complementary DNA microarray from our laboratory to examine the time-dependent profiles of gene expression in Arabidopsis roots and shoots. From this, we identified 282 hypoxia-responsive genes. These included novel genes for a zinc finger protein, WRKY family transcription factor, and glycosyl hydrolase as well as those previously identified as hypoxia-related genes including alcohol dehydrogenase (ADH), pyruvate decarboxylase (PDC), and phosphofructokinase. Cluster analysis of these profiles suggested that the hypoxia response occurs in two distinctive phases: early and late. The early response to imposed stress (hours 1, 3, and 8) includes increased expression of fermentation-related genes and transcription factors, such as by members of the $C_2H_2$ zinc finger family and WRKY family. The late response (hours 24 and 72) involves the down-regulation of genes that function in secondary metabolic pathways and up-regulation of transcription factors that are mostly related to the ethylene-responsive element binding protein family. Mutants of Arabidopsis defective in sucrose synthase1 (SUS1), the At1g05060 gene (with unknown function), ADH, and the WRKY33 were more sensitive to hypoxic stress, evidence of the importance of these genes in that response. The genes presented here allow us to deepen our understanding of the mechanism for this stress response and, eventually, will aid in the development of more flood-tolerant crops.