Glycogen is a major reserve carbohydrate in both prokaryotes and eukaryotes, and starch is a major reserve carbohydrate only in photosynthetic eukaryotes. Synthesis of both glycogen and starch involves at least glycogen (starch) synthase and branching enzyme, as well as perhaps debranching enzyme. Extensive biochemical and genetic research has been carried out on glycogen and starch biosynthesis in bacteria and plants; however, it is not yet understood what controls the structure of these two glucans to result in such different forms or how glycogen synthesis (certainly more ancient) gave rise to starch synthesis. This phylogenetic study on the evolutionary relationships of bacterial glycogen synthases with plant starch synthases and bacterial glycogen debranching enzymes with plant isoamylases, combined with the published studies of the origin of plastids in higher plants from an endosymbiotic event, reveal a close evolutionary relationship between glycogen and starch biosynthesis and suggest a potential origin for starch biosynthesis.