Branched polymers of glucose are universally used for energy storage in cells, taking the form of glycogen in animals, fungi, Bacteria, and Archaea, and of amylopectin in plants. Some enzymes involved in glycogen and amylopectin metabolism are similarly conserved in all forms of life, but some, interestingly, are not. In this paper we focus on phylogeny of glycogen branching and debranching enzymes, respectively involved in introducing and removing of the alpha(1->6) bonds in glucose polymers, bonds that provide the unique branching structure to glucose polymers. Results: We performed a large scale phylogenomic analysis of branching and debranching enzymes in over 400 completely sequenced genomes, including more than 200 from eukaryotes. We show that branching and debranching enzymes can be found in all kingdoms of life, including all major groups of eukaryotes, and thus were likely to have been present in the last universal common ancestor (LUCA) but have been lost in seemingly random fashion in numerous single celled eukaryotes. We also show how animal branching and debranching enzymes evolved from their LUCA ancestors by acquiring additional domains. Furthermore, we show that enzymes commonly perceived as orthologous, such as human branching enzyme GBE1 and E. coli branching enzyme glgB, are in fact related by a gene duplication and consequently paralogous. Conclusions: Despite its well known association with animal liver cells and plant starch, energy storage in the form of branched glucose polymers is clearly an ancient process and has been present in the earliest cells. The evolution of enzymes enabling this form of energy storage is more complex than previously thought and illustrates the need for explicit phylogenomic analysis in the study of even seemingly "simple" metabolic enzymes. Patterns of conservation and divergence in the evolution of the glycogen/starch branching and debranching enzymes have interesting biomedical connotations, as mutations in these enzymes lead to a variety of inheritable diseases in humans and other mammals.