The Rhodophyta (red algae) and Chlorophyta (green algae) form a natural group of algae in that they have chloroplasts surrounded by only the two membranes of the chloroplast envelope. The evolutionary event that led to the chloroplast occurred as follows (Fig. III.1). A phagocytotic protozoan took up a cyanobacterium into a food vesicle. Instead of being digested as a source of food, the cyanobacterium lived as an endosymbiont in the protozoan. This event benefited the protozoan because it received some of the photosynthate from the endosymbiotic alga, and it benefited the cyanobacterium because it received a protected stable environment. Through evolution the wall of the endosymbiotic cyanobacterium was lost. A mutation in the endosymbiont which resulted in a loss of the wall would have been selected for in evolution because it would have facilitated the transfer of compounds between the host and the endosymbiont. The food vesicle membrane of the phagocytotic host became the outer membrane of the chloroplast envelope. The plasma membrane of the cyanobacterium symbiont became the inner membrane of the chloroplast envelope. Rearrangement of the thylakoid membranes and evolution of polyhedral bodies into a pyrenoid completed the transition to a true chloroplast such as occurs in extant green and red algae.

The endosymbiotic origin of chloroplasts was first proposed by the Russian biologist Konstantin Mereschkowsky (1855–1921) (Fig. III.2) with the fundamentals of the idea appearing in his 1905 work, The Nature and Origins of Chromatophores in the Plant Kingdom (see Martin and Kowallik, 1999, for English translation).