The endosymbiotic theory proposes that mitochondria and chloroplasts originated as:

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Free-living prokaryotes that were engulfed by ancestral eukaryotic cells and developed a symbiotic relationship. The endosymbiotic theory, championed by Lynn Margulis in the 1960s, proposes that mitochondria and chloroplasts originated as free-living prokaryotic organisms that were engulfed by ancestral eukaryotic cells through endocytosis. Rather than being digested, these engulfed prokaryotes survived inside the host cell and developed a mutually beneficial (symbiotic) relationship. Over evolutionary time, the endosymbionts transferred most of their genes to the host cell's nucleus while retaining some of their own DNA, eventually becoming the organelles we know today.

The invagination hypothesis (that organelles formed from infoldings of the plasma membrane) is an alternative theory for the origin of some endomembrane system components but does not explain mitochondria and chloroplasts, which have strong prokaryotic features. The idea that organelles originated as nuclear fragments does not explain the double membranes, circular DNA, or prokaryotic-type ribosomes found in these organelles. The suggestion that viral particles integrated into cells describes a different evolutionary process (endogenization) that does occur but is not the origin of mitochondria and chloroplasts.

Multiple lines of evidence support the endosymbiotic theory: mitochondria and chloroplasts have their own circular DNA (similar to bacterial chromosomes), replicate independently by binary fission (like bacteria), have double membranes (the inner membrane from the original prokaryote, the outer from the host cell's engulfing membrane), have their own ribosomes that resemble bacterial ribosomes (70S) rather than eukaryotic cytoplasmic ribosomes (80S), and are similar in size to bacteria. Molecular phylogenetic analyses confirm that mitochondria are related to alpha-proteobacteria and chloroplasts are related to cyanobacteria. The endosymbiotic theory is one of the most well-supported theories in biology and is important for the CLEP Biology exam.

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