Reactive oxygen species (ROS) play an important role as triggers of gene expression during biotic and abiotic stresses, among which is low oxygen (O 2 ). Previous studies have shown that ROS regulation under low O 2 is driven by a RHO-like GTPase that allows tight control of hydrogen peroxide (H 2 O 2 ) production. H 2 O 2 is thought to regulate the expression of heat shock proteins, in a mechanism that is common to both O 2 deprivation and to heat stress. In this work, we used publicly available Arabidopsis (Arabidopsis thaliana) microarray datasets related to ROS and O 2 deprivation to define transcriptome convergence pattern. Our results show that although Arabidopsis response to anoxic and hypoxic treatments share a common core of genes related to the anaerobic metabolism, they differ in terms of ROS-related gene response. We propose that H 2 O 2 production under O 2 deprivation is a trait present in a very early phase of anoxia, and that ROS are needed for the regulation of a set of genes belonging to the heat shock protein and ROS-mediated groups. This mechanism, likely not regulated via the N-end rule pathway for O 2 sensing, is probably mediated by a NADPH oxidase and it is involved in plant tolerance to the stress.