We have characterized four pea mitochondrial DNA segments carrying the F1ATPase alpha-subunit coding sequences. These four types share a common 1.7-kb repeat sequence flanked by four combinations of two different left- and right-hand sequences. These results suggest that the alpha-subunit genes locate at the homologous recombination sites in the pea mitochondrial genome and that homologous recombination between two of these loci generates the other two types of structures. The uninterrupted alpha-subunit coding sequence of 1,521 bp is present in two of these loci. A rearrangement of 965 bp 3' to the ATG initiation codon generates two copies of pseudogenes where the C-terminal two-thirds of the alpha-subunit coding sequence is replaced with an unidentified coding frame. The other border of sequence divergence is located 733 bp upstream of the ATG initiation codon. Although multiple forms of alpha-subunit gene transcripts are present in mitochondria, the pseudogenes do not seem to express any alpha-subunit-related polypeptide.