Sponge transcriptomes are important resources for studying the stress responses of these ecologically important filter feeders, the interactions between sponges and their symbionts, and the evolutionary history of metazoans. Here, we generated reference transcriptomes for two common and cosmopolitan Indo-Pacific sponge species: Carteriospongia foliascens and Cliona orientalis. We also created a reference transcriptome for the primary symbiont of C. orientalis—Gerakladium endoclionum. Assemblies for C. foliascens, C. orientalis, and G. endoclionum contained 67,304, 82,895, and 28,670 contigs, respectively. Contigs represented 15,248–37,344 isogroups (~ genes) per assembly, and N50s ranged from 1672–4355 bp. Sponge transcriptomes were high in completeness and quality, with an average of 93% of core EuKaryotic Orthologous Groups (KOGs) and 98% of single-copy metazoan core gene orthologs identified. The G. endoclionum assembly was partial with 56% of core KOGs and 32% of single-copy eukaryotic core gene orthologs identified. These reference transcriptomes provide a valuable resource for future research assessing sponge stress responses.