The organization of the mitochondrial genome of higher plants is complex. It has two striking features: a large size that can vary among plant species; and the ability to undergo homologous recombination that results in variation within species. From cosmid clone mapping studies, the total genetic information of the plant mitochondrial genome can be arranged into a single circular molecule that is referred to as the master chromosome. This circular DNA molecule contains repeated sequences that can generate, via intramolecular recombination, either isomeric forms of the master chromosome or smaller subgenomic circular DNA molecules. The maize mitochondrial genome is the most complex and largest mitochondrial genome for which a physical map is presently available. Its organization varies considerably among the different maize cytotypes. In an attempt to understand the numerous different mitochondrial DNA rearrangements encountered among those cytotypes, we have proposed a general model of genome evolution that can explain a multitude of genomic rearrangements, not only for the maize mitochondrial DNA but also for other higher plant mitochondrial genomes as well.