Mitochondria, the energy-producing organelles of eukaryotic cells, evolved from an endosymbiotic α-Proteobacterium more than one billion years ago. These organelles contain their own genetic system, a remnant of the endosymbiont’s genome that varies considerably in size, genome architecture, and coding capacity throughout eukaryotes. The five to ~100 genes contained in mitochondrial DNA (mtDNA) code for mitochondrial components involved in up to five mitochondrial processes: respiration/oxidative phosphorylation and translation (invariantly), as well as transcription, RNA maturation, and protein import. These mtDNA-encoded proteins have provided an invaluable alternative to nuclear gene sequences as a source for molecular phylogenetics, by both elucidating and confirming relationships among eukaryotes. However, only a small fraction of the mitochondrial proteome is encoded by the mitochondrion. Indeed, nuclear genes code for much of the proteome. It is likely that most of these genes migrated from the mitochondrion to the nucleus over the course of eukaryotic evolution. In some cases, however, it is clear that genes were recruited to the mitochondrion from the nucleus or other undefined sources. New insights into early mitochondrial genome evolution come from both the investigation of primitive (minimally derived) eukaryotes and the comparison of mitochondria to intracellular bacterial symbionts. Defining more precisely both the α-proteobacterial ancestry of the mitochondrial genome and the contribution of the endosymbiotic event to the nuclear genome will be essential for a full understanding of the origin and evolution of the eukaryotic cell as a whole.