Ethylene plays essential roles in rice adaptive responses to water-saturating environment. Here, through analysis of the ethylene-insensitive mutant mhz1, we discovered that a histidine kinase MHZ1positively regulates ethylene responses in rice roots. MHZ1 autophosphorylates at the conserved histidine and can transfer the phosphoryl signal to response regulator OsRR21 via phosphotransfer proteins OsAHP1/2. And the phosphorelay is required for ethylene signaling. Ethylene receptor OsERS2, via GAF domain, physically interacts with MHZ1 to inhibit its kinase activity, subsequently the MHZ1-mediated phosphorelay. We propose that MHZ1 mediates ethylene response in a way partially independent of OsEIN2, and is directly inhibited by ethylene receptors. The resultssuggest that rice may have evolved to adopt the MHZ1 pathway in a different mechanism to strongly control ethylene-regulated root growth for adaptation in water environment.