High-throughput sequencing technologies, such as RNA sequencing (RNA-Seq), have greatly enhanced our ability to sequence and characterize the transcriptome of nonmodel organisms. The ability to study expression of thousands of genes in highly threatened yet understudied organisms holds great potential for advancing the field of conservation biology. Despite rapid gains in our analytical abilities and understanding of the physiological underpinnings of the organism, genomic resources remain limited for nonmodel organisms such as freshwater mussels, one of the most imperiled groups of animals worldwide. Here we provide the first characterization of the transcriptome of the North American freshwater mussel Amblema plicata (threeridge) using an RNA-Seq approach. Gill tissue samples were collected from mussels in the Muskingum River in Washington County, Ohio, USA. RNA was extracted and sequenced on the Illumina HiSeq 2500 sequencer with output as 100-base-pair paired-end reads. De novo assembly of sequenced reads was performed using Trinity. Assembled transcripts were used as BLASTx queries against the National Center for Biotechnology nonredundant database, and functional annotation using gene ontology (GO) terms was performed using Blast2GO. Transcriptome assembly produced 264,027 transcripts. Of these transcripts, 54,331 (20.58%) received BLAST hits and 22,223 were annotated with GO terms. We provide examples of identified candidate genes that may be useful for studying physiological responses of freshwater mussels to various environmental stressors, such as temperature, hypoxia, and pollutants. The A. plicata transcriptome improves the genomic resources available for freshwater mussels, and may aid in the development of molecular tools, with the ultimate goal of increasing our understanding of freshwater mussel physiology and improving conservation techniques.