In the Gulf of Maine the rocky intertidal blue mussel Mytilus edulis (Linnaeus, 1758) is one of the most important ecosystem engineers in these communities and have been the subject of numerous physiological and ecological studies. There is now abundant support that global climate change is occurring at unprecedented rates in the GOM. In a world where multiple environmental factors vary simultaneously, we need to be able to quantify the underlying physiological, biochemical, and molecular changes that lead to emergent properties of the organism (e.g., growth, reproduction, mortality) in key species like intertidal mussels. Here, we provide transcriptomic resources for both the gill and adductor muscle of blue mussels from the GOM. Of the full complement of transcripts (n = 57,718), 56,655 were expressed in the gill and 53,081 were expressed in the adductor muscle with 4,489 and 915 transcripts expressed uniquely in the gill and muscle, respectively. The putative transcripts for M. edulis were assigned to 617 genes for gill and 178 genes for adductor muscle and clustered into 12 functional categories, including those in well-known stress pathways. These transcriptomes can be used to test important hypotheses on gene regulation, phenotypic plasticity, mechanisms of physiological resilience, and local adaptation in response to climate change stressors (i.e., thermal stress and ocean acidification).