We have adopted a hypoxic treatment system in which only roots were under hypoxic conditions. Through analyzing global transcriptional changes in both shoots and roots, we found that systemic signals may be transduced from roots to trigger responses in tissues not directly subjected to hypoxia. The molecular mechanisms of such systemic responses under flooding are currently largely unknown. Using ontological categorization for regulated genes, a systemic managing program of carbohydrate metabolism was observed, providing an example of how systemic responses might facilitate the survival of plants under flooding. Moreover, a proportion of gene expressions that regulated in shoots by flooding was affected in an ethylene signaling mutation, ein2-5. Many systemic-responsive genes involved in the systemic carbohydrate managing program, hormone responses and metabolism, ubiquitin-dependent protein degradation were also affected in ein2-5. These results suggested an important role of ethylene in mediation of hypoxic systemic responses. Genes associated with abscisic acid (ABA) biosynthesis are upregulated in shoots and down regulated in roots. An ABA signaling mutation, abi4-1, affects expression of several systemic responsive genes. These results suggested that regulation of ABA biosynthesis could be required for systemic responses. The implications of these results for the systemic responses of root-flooded Arabidopsis are discussed.