A variety of secondary metabolites with promising antimicrobial and anti-tumor properties have been identified in marine organisms. Sponges, in particular, have been the source of several of these, including discodermolide from Discodermia dissoluta. While metagenomic studies have been undertaken to identify genes involved in discodermolide production, presently, a transcriptomic approach has not been taken to characterize the metagenome of D. dissoluta. Samples of D. dissoluta were collected from a site in the Bahamas and screened for secondary metabolite production. Some specimens of D. dissoluta were positive for discodermolide while others were not. In order to determine which genes are differentially expressed between the two specimens, suppression subtractive hybridization (SSH) was performed utilizing a chemistry negative and chemistry positive morphotype as the “driver” and “tester” populations respectively. Here we demonstrate the efficacy of SSH through the identification of transcripts related to symbiosis and secondary metabolite production by metatranscriptomic and bioinformatics analyses of the resulting subtracted library as well as a 16S rRNA library. Additionally, we have confirmed differential gene expression of selected sequences utilizing quantitative polymerase chain reaction (qPCR) with SYBR Green chemistry to screen and characterize genes, some of which appear to be related to novel metabolism and unknown functions related to symbiosis within the complex sponge-microbial community.