A novel ATP synthase gene from soybean has been cloned and characterized. A subunit from the FA portion of the complex is encoded by two nuclear genes. The genomic clone(s) contain five exons encoding a protein of 179 amino acids. The amino terminal end contains many properties of a mitochondrial targeting sequence and preliminary in vitro import studies indicate that there is a cleavable precursor of approximately 30 amino acids. The predicted protein sequence shows high homology with the N-terminal sequence from an isolated subunit of ATP synthase complex from spinach (Hamsaur and Glaser (1992) Eur. J. Biochem. 205, 409-416). The subunit was tentatively identified as the equivalent of subunit d in bovine and P18 in yeast based on structural identity.