Phototrophic eukaryotes were established by the engulfment of oxygenic phototrophic prokaryotes (cyanobacteria) by a heterotrophic host. This process, called primary endosymbiosis, gave rise to the taxon Archaeplastida, which comprises green plants, rhodophytes and glaucophytes. Further rounds of endosymbiotic events produced a variety of phototrophic organisms, which could accumulate α-1,4-/α-1,6-glucans (including starch) or β-1,3-/β-1,6-glucans. In this article, we review the recent progress in the study of the intracellular localization and molecular forms of storage glucan, especially starch, among the known phototrophs and related organisms.