Cytoplasmic male sterility (CMS) represents an important agricultural trait in pearl millet [Pennisetum glaucum (L.) R. Br.] with a value to the seed industry in facilitating economical hybrid seed production. Among the CMS systems available in millet, the A1 source is the most commonly used for hybrid production, but it can undergo low frequency reversion to fertility. Plant mitochondrial genomes are highly recombinogenic, becoming unstable and prone to ectopic recombination under conditions of tissue culture, somatic hybridization, or interspecific crossing. Similarly, CMS systems prone to spontaneous fertility reversion experience sporadic mitochondrial genome instability. We compared mitochondrial genome configurations between the male-sterile A1 line and fertile revertants of pearl millet to develop a model for millet mitochondrial genome reorganization upon reversion. Relative copy number of a subgenomic molecule containing the CoxI-1-2 junction region, a component of the recombination process for reversion, is amplified tenfold following reversion, relative to the CMS A1 line. We propose that increased copy number of this molecule in a small number of cells or at low frequency triggers a recombination cascade, likely during reproductive development. The proposed recombination process initiates with ectopic recombination through a 7-bp repeat to produce a novel CoxI-3-2 junction molecule and an unstable recombination intermediate. Subsequent intra-molecular recombination stabilizes the intermediate to form a new copy of CoxI accompanied by a deletion. This study furthers the argument that substoichiometric shifting within the plant mitochondrial genome plays an important role in the evolution of the mitochondrial genome and plant reproductive dynamics.