Viola yedoensis Makino is an important Chinese traditional medicine plant adapted to cadmium (Cd) pollution regions. Illumina sequencing technology was used to sequence the transcriptome of V yedoensis Makino. We sequenced Cd-treated (VIYCd) and untreated (VIYCK) samples of V yedoensis, and obtained 100,410,834 and 83,587,676 high quality reads, respectively. After de nova assembly and quantitative assessment, 109,800 unigenes were finally generated with an average length of 661 bp. We then obtained functional annotations by aligning unigenes with public protein databases including NR, NT, SwissProt, KEGG and COG. In addition, 892 differentially expressed genes (DEGs) were investigated between the two libraries of untreated (VIYCK) and Cd-treated (VIYCd) plants. Moreover, 15 randomly selected DEGs were further validated with qRT-PCR and the results were highly accordant with the Solexa analysis. This study firstly generated a successful global analysis of the V yedoensis transcriptome and it will provide for further studies on gene expression, genomics, and functional genomics in Violaceae. (C) 2015 Elsevier Inc. All rights reserved.