Ascidians are a notable source of nitrogen-bearing secondary metabolites with a wide range of biological activities. Although many biologically active compounds have been isolated from ascidians, it is often unclear whether the animal or associated microbial symbionts such as bacteria or fungi are the true biosynthetic source of the metabolites. We have addressed the question of the biosynthetic source of the alkaloids granulatimide and isogranulatimides by localizing these compounds within the ascidian. In this work, we demonstrate that granulatimide is stored in Didemnumgranulatum tunic bladder cells. Analysis by confocal fluorescence microscopy at the granulatimide emission range indicated the presence of fluorescent cells as highly vacuolated cells found dispersed in the ascidian tunic. Since this is the most exposed ascidian tissue, it is possible that these alkaloids may have a protective role, either as sunscreens and/or as feeding deterrents.