Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is uniform in size, gene content, and organization. However, data collected in the last decade have challenged this view by revealing substantial diversity in animal mitochondrial genomes. Much of this diversity is found in non-bilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the major branches of the animal tree along with Bilateria. Within these phyla, mtDNA shows substantial variation in size, organization, genetic code, gene content, presence/absence of introns, tRNA structures, mRNA processing, and rates of evolution. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.