In higher plants under low oxygen or hypoxic conditions, the phytohormone ethylene and hydrogen peroxide (H2O2) are involved in complex regulatory mechanisms in hypoxia signaling pathways. The respiratory burst oxidase homolog D (RbohD), an NADPH oxidase, is involved in the primary stages of hypoxia signaling, modulating the expression of downstream hypoxia-inducible genes under hypoxic stress. In this study, our data revealed that under normoxic conditions, seed germination was delayed in the rbohD/ein2-5 double mutant, whereas postgermination stage root growth was promoted. Under submergence, the rbohD/ein2-5 double mutant line had an inhibited root growth phenotype. Furthermore, chlorophyll content and leaf survival were reduced in the rbohD/ein2-5 double mutant compared with wild-type plants under submerged conditions. In quantitative RT-PCR analysis, the induction of Ethylene-responsive factor 73/hypoxia responsive 1 (AtERF73/HRE1) and alcohol dehydrogenase 1 (AtADH1) transcripts was lower in the rbohD/ein2-5 double mutant during hypoxic stress than in wild-type plants and in rbohD and ein2-5 mutant lines. Taken together, our results indicate that an interplay of ethylene and RbohD is involved in regulating seed germination and post-germination stages under normoxic conditions. Moreover, ethylene and RbohD are involved in modulating seedling root growth, leaf chlorophyll content, and hypoxia-inducible gene expression under hypoxic conditions.