The mitochondrial DNA of the bowfin fish and each of two species of treefrogs displays large-scale size variation. Within each species, mitochondrial genomes span more than a 700 base pair range, and the size polymorphism is localized to one portion of the genome. In addition, about 5 percent of the total 357 individuals surveyed were observed to carry two size classes of mtDNA. These findings are among the few documented instances of extensive within-species mtDNA size polymorphism and individual heteroplasmy, and constitute exceptions to previously reached generalizations about the molecular basis of mtDNA variation.