Abstract Eukaryotes likely originated from an endosymbiosis between an α-protobacterium and an Asgard archaeal host. Although endosymbiosis was followed by massive gene transfer from the mitochondrial DNA (mtDNA) to the nuclear genome, mtDNA was retained in most eukaryotes. Since the early 1980s, the genetic variation, species diversity and functional implications of mtDNA’s genetic content have been extensively studied. Here, we assemble articles that discuss recent advances and new insights in