Abstract Mitochondria have their own genetic system – a vestigial genome originating from an endosymbiotic α-proteobacterial ancestor. The genetic function of mitochondrial DNA (mtDNA) is well-conserved, being involved in a maximum of five mitochondrial processes: invariantly in respiration and/or oxidative phosphorylation and translation, and also in transcription, RNA maturation and protein import. Recent data from mitochondrial genomics research demonstrate that this genetic conservatism contrasts with an often-perplexing diversity in structure and gene expression mechanisms. In addition to outlining the extraordinary diversity of mtDNA, this review highlights the divergent trends in mitochondrial genome evolution in the various eukaryotic lineages, and examines the relationship between mitochondrial and nuclear genome evolution in a given organism.