The tropical sponge Dysidea granulosa contains a number of symbiotic heterotrophic bacteria and large quantities of the photosynthetic cyanobacterium Oscillatoria spongeliae, which are reported to be responsible for the production of ecologically active polybrominated diphenyl ethers (BDEs) in Dysidea spp. In order to better understand the relationship between these symbionts and the production of BDEs, we looked at the variation in secondary chemistry in 3 populations of D. granulosa and the relationship between cyanobacteria and secondary chemistry in the sponge, and experimentally assessed the role that depth and light play in this relationship by transplanting sponges in the field. At a population scale, the concentration of BDEs is positively correlated with the concentration of chlorophyll a (chl a), both varying significantly between populations. Yet, in sponges experimentally transplanted to a deeper site, the concentration of chl a decreased significantly while BDE concentration remained stable. We specifically tested the importance of light in determining levels of symbionts and BDEs by placing sponges under transparent, UV-opaque, and black Plexiglas plates. After 5 wk, levels of BDEs and chl a had decreased significantly, although these trends differed between light treatment, suggesting a lack of direct correlation between BDEs and cyanobacterial populations. This was also supported by a within-sponge analysis of chl a and BDEs, since high levels of compounds were found in the choanosome of the sponge, whereas chl a and cyanobacterial contents were minimal. Our data suggest that the relationship between the levels of BDEs in D. granulosa and its photosynthetic symbionts is more complex than expected. Variation in the levels of secondary metabolites and symbionts seems to be related at a population scale, but unrelated at an individual scale.