Mitochondrial F(1)F(0)-ATP synthase is a key enzymatic complex of energy metabolism that provides ATP for the cell. Subunits of this enzyme over-express under stress conditions. Little is known about the structure and regulatory mechanism of the F(0) portion of this enzyme. We isolated the full-length coding sequence of the RMtATP6 gene from rice and wheat, and partial sequences from Aegilops crassa and Triticum monococcum (Poaceae). We found that the sequence of rice RMtATP6 is 1965 bp long and contains two exons and one intron in 3'-UTR. Then, we analyzed the 2000-bp upstream region of the initiation codon ATG of the RMtATP6 and AtMtATP6, as promoter. The RMtATP6 coding sequence was found to be much conserved in the different plant species, possibly because of its key role under stress conditions. Promoter analysis demonstrated that RMtATP6 and AtMtATP6 include cis-acting elements such as ABRE, MYC/MYB, GT element in the upstream region, which respond to abscisic acid stress hormone and might show vital its roles in biotic and abiotic tolerance as an early-stress responsive gene. A mitochondrial signal peptide of 30 amino acids in length and an N-terminal cleavage site between amino acids 20 and 21 were discovered in RMtATP6. In addition, we found a transmembrane domain with an alpha helix structure that possibly passed through the mitochondrial inner membrane and established the 6-kDa subunit in the F(0) portion of the enzyme complex. Apparently, under stress conditions, with increasing ATP consumption by the cell, the 6-kDa subunit accumulates; by switching on F(1)F(0)-ATP synthase it provides additional energy needed for cell homeostasis.