Developing genomic resources for species used as bioindicators of environmental pollution facilitates identification of new biomarkers of interest. The variegated scallop Mimachlamys varia (Pectinidae) is a marine bivalve used to evaluate and monitor chemical contamination on the French Atlantic coast. Because natural populations of this species are commercially harvested, there is particular interest in understanding its responses to environmental pollution and pathogens. We assembled and annotated the transcriptome of M. varia obtained from a pool of five tissue types (gills, mantle, digestive gland, gonad, adductor muscle). In depth Illumina sequencing led to the assembly of 333,022 transcripts, covering 98% of genes conserved among eukaryotes.