Fluorescent natural compounds have been identified in several marine hosts of microalgae. Their prevalence, and the energy the host is expending on their synthesis, suggests an important, yet poorly understood ecological role. It has been suggested that some of these natural products may enhance the photosynthesis of microbial symbionts. In this study, the effect of Ageladine A (Ag A), a pH-dependent fluorophore found in sponges of the genus Agelas, on the photosynthesis of nine microalgal species and strains was examined. The data showed that the variety of effects of Ag A additions differed between species, and even strains within a species. While in one strain of Synechococcus sp., the presence of Ag A increased gross photosynthesis under UV light exposure, it decreased in another. And while in the chlorophyte T. chuii overall metabolic activity was greatly reduced under all forms of lighting, photosynthesis in T. lutea was positively affected by the addition of Ag A. The variety of effects of Ag A on photosynthesis observed in this study indicate a complex interaction of Ag A with microalgal cells and suggests that a host may be able to shape its own symbiotic microbiome with self-produced natural products.