The union of an archaeon and a proteobacterium at the origin of eukaryotic cell was a transformative event in the history of Earth that made evolution of complex life possible. Mitochondria are the most recognizable vestige of that event as they are semi-autonomous organelles with their own genome. Although the primary function of mitochondria – the production of energy by oxidative phosphorylation – is mainly conserved across the tree of life, their structure, genome organization, and secondary functions show substantial variation. Recently, we surveyed some of this variation in animal mitochondrial DNA (mtDNA). Although animal mtDNA is typically described as a uniform molecule, we discovered substantial differences in its size, organization, genetic code, gene content, presence/absence of introns, tRNA structures, mRNA processing, and rates of evolution. Much of that diversity was found in four phyla non-bilaterian animals (Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the major branches of the animal tree along with Bilateria. We also found that the changes in animal mitochondrial DNA organization correlate closely with changes in the composition of mitochondrial proteins that are encoded in the nucleus but imported to mitochondria. Currently, we are using several bioinformatics approaches to identify and characterize the full mitochondrial proteome in major animal lineages.