<jats:p>In several marine hosts of microalgae, fluorescent natural products may play an important role. While the ecological function of these compounds is not well understood, an interaction of these molecules with the photosynthesis of the symbionts has been suggested. In this study, the effect of Ageladine A (Ag A), a pH-dependent fluorophore found in sponges of the genus <jats:italic>Agelas</jats:italic>, on microalgal fluorescence was examined. The spectra showed an accumulation of Ag A within the cells, but with variable impacts on fluorescence. While in two <jats:italic>Synechococcus</jats:italic> strains, fluorescence of phycoerythrin increased significantly, the fluorescence of other <jats:italic>Synechococcus</jats:italic> strains was not affected. In four out of the five eukaryote species examined, chlorophyll <jats:italic>a</jats:italic> (Chl <jats:italic>a</jats:italic>) fluorescence intensity was modulated. In <jats:italic>Tisochrysis lutea</jats:italic>, for example, the position of the fluorescence emission maximum of Chl <jats:italic>a</jats:italic> was shifted. The variety of these effects of Ag A on microalgal fluorescence suggests that fluorophores derived from animals could play a crucial role in shaping the composition of marine host/symbiont systems.</jats:p>