Transgenic Arabidopsis plants (IPT) containing the SAG12:ipt autoregulated cytokinin production capability accumulate more cytokinin and remain greener and produce more biomass and seeds than wild-type (WT) plants under flooding stress. To gain insight into changes in gene expression that contribute to flooding tolerance, whole genome microarray analysis of the 27,000 Arabidopsis genes was conducted at specific times during a 5 d period of non-flooded control, waterlogging, and complete submergence. Statistical analysis by ANOVA identified a group of 1078 genes that were up-regulated in both genotypes under submergence stress. Gene Ontology (GO) analysis of the categorical functions of the up-regulated genes showed a group of 96 genes involved in the regulation of transcription (p= 5.95E-06), and a group of 55 genes in signal transduction (p=1.41E-03). Hierarchical clustering using Euclidean distance metric revealed distinct temporal patterns of expression in these genes: 1) Late induction genes whose level of expression increased gradually during the 5 d submergence; 2) Early induction genes whose expression was induced to a high level at 1 h of submergence but declined thereafter; 3) Constant expression genes whose expression was induced to a low level at 1 h of submergence and remained constant throughout the 5 d submergence. Under submergence stress, genes of photosynthesis and energy utilization pathways expressed 2- to 4-fold more in the tolerant IPT plants than in WT plants suggesting that flooding tolerance mechanisms involve both energy production and utilization. Comprehensive analysis of transcriptional changes associated with cytokinin-induced flooding stress tolerance will be reported.