Mitochondria are membrane-enclosed organelles present in most eukaryotic cells that generate most of the cell's adenosine triphosphate (ATP) supply. Derived from a proteobacterial ancestor, mitochondria harbour their own, drastically reduced genome. Starting from a prokaryote-like ancestral state encoding a complete ribosomal ribonucleic acid (rRNA) operon, a complete set of transfer RNAs (tRNAs) required for translation, and key enzymes of the respiratory chain as well as some ribosomal proteins, the mitogenome has been dramatically restructured and further reduced in many of the eukaryotic lineages. The loss and transfer to the nucleus of mitochondrial genes is a common trend in most phyla, in particular in Metazoa and Alveolata. In extreme, phylogenetically dispersed cases, often associated with parasitic or anaerobic life styles, mitochondria have been transformed to the so-called mitosomes or hydrogenosomes devoid of their own genetic material. Ancestrally a single circular deoxyribonucleic acid (DNA), mitogenomes have evolved to complex, fragmented architectures in particular in Euglenozoa.