Mitochondria — the so-called “powerhouse of the cell” — hold a special place in eukaryotic (nucleus-containing) cells. Evidence accumulated over the past half century strongly points to an origin of the mitochondrion from a free-living bacterium closely related to a specific group, the Alphaproteobacteria. However, the actual processes by which this endosymbiotic bacterium was integrated into its host cell remain controversial. So, what do we really know?