According to the endosymbiont hypothesis, mitochondria and chloroplasts are the evolutionary descendants of free-living prokaryotes, which during evolution have been stripped of practically all functions except those related to energy transduction. Some prokaryotic organisms have features similar to those of energy-transducing organelles: Paracoccus denitrificans, an aerobic bacterium, has an electron transport chain like that in mitochondria, and Prochloron, a green photosynthetic bacterium, has a light trapping system (with chlorophyll b) like that found in chloroplasts in higher plants.

It is envisaged that the modern eukaryotic animal cell arose from the emergence of a nucleated cell dependent on glycolytic fermentation for its ATP supply and separately from the emergence of a nucleated bacterial cell, possessing a respiratory chain and therefore a more efficient method of producig ATP. Early in the evolutionary timescale, the nucleated cell either absorbed or was invaded by the bacterial cell. Initially, a stable endo-symbiotic relationship was established which conferred advantages over the free living nucleated cells or anucleated cells. Such an arrangement is seen even today in the giant amoeba Pelomyxa palustris, which lacks mitochondria but contains respiring endosymbiotic bacteria. During the evolution of eukaryotic cells the nuclear genome has absorbed most of the genome of the anucleated organism. The plant cell is probably a descendant of this cell, which some time early on in evolution, absorbed a second prokaryotic cell capable of carrying photophosphorylation.