Mollusks are the largest group of marine invertebrates and are known to harbor bacterial communities; however, the characterization and metabolic roles of these communities to the biology of mollusks are unknown. Sacoglossan sea slugs are herbivorous mollusks well known for their unique ability among metazoans to sequester functional chloroplasts from their algal food through a process called kleptoplasty, enabling a few species of these slugs to photosynthesize. Sacoglossan mollusks are also known to sequester chemical compounds from their algal diets through a process called kleptochemistry and use these compounds as defense molecules. These defense molecules often display medicinal properties. The mechanisms for such phenomena are unknown. I characterized the bacterial communities associated with the Hawaiian sea slug Elysia rufescens and its algal diet Bryopsis sp., in which the promising anticancer compound, Kahalalide F (KF) was extracted, through both culture-based and molecular analysis. I cultured a total of 460 bacteria from the mollusk and Bryopsis and screened them for KF production. I found a diverse assemblage of bacteria associated with this sacoglossan comprising 16 different bacterial phyla. In addition, a photosynthetic sacoglossan slug, Elysia crispata from two Caribbean locations and their associated alga bacterial communities were characterized. I discovered less bacterial diversity associated with this sacoglossan and found that the bacterial communities associated with E. crispata from different locations are more similar to each other than the bacterial communities of the associated alga. This work forms the basis for describing the bacterial community of the sacoglossans E. rufescens and E. crispata and furthers our understanding of the potential roles bacteria may play in the unusual sacoglossan niche.