Sponge and sponge symbionts produce a diverse array of natural products. Microbial symbionts are hypothesized to benefit their sponge hosts in several ways, including the production of secondary metabolites many of which remain structurally uncharacterized. We examined the relationship between symbiont community structure and secondary metabolite profiles in the common Chesapeake Bay sponges Clathria prolifera and Halichondria bowerbanki. C. prolifera produces high concentrations of diverse carotenoid compounds giving the sponge a bright red color. The carotenoids are hypothesized to protect the sponge from environmental stressors such as UV radiation. We quantified carotenoid concentrations during a 12 month period using both UV/VIS and HPLC methodologies. The temporal stability of host-symbiont association is poorly understood, and it is unknown whether natural changes in the symbiont community leads to changes in secondary metabolite profiles. To begin to assign particular compounds with the microbial symbiont responsible for the production of that compound, we cultured pigmented microbes isolated from sponge larvae. We isolated unique bacterial symbionts from the larvae of H. bowerbanki and investigated the structural and spectroscopic characteristics of specific non-carotenoid secondary metabolites. Our results provide insights into the nature of the sponge-symbiont association under fluctuating environmental conditions. Understanding these relationships has important practical consequences because many compounds produced by sponges have the potential to be beneficial as lead compounds for the pharmaceutical industry.