Significance Diatoms contribute considerably to the primary productivity of aquatic ecosystems. In diatoms, the principal storage polysaccharide is chrysolaminarin, consisting of branched β-1,3-glucans. The β-1,3-glucans are distributed widely in organisms and, besides starch and glycogen, represent major storage polysaccharides in nature. However, the synthesis pathway of storage β-1,3-glucans is still unclear. We report the localization of the glucan synthase, and thus the elongation of the glucan polymer, in the tonoplast membrane of the diatom Phaeodactylum tricornutum . Reduced expression of this glucan synthase results in various cellular effects. Our data indicate that the capacity of vacuolar polysaccharide storage substantially influences the photosynthetic performance of the plastid.