The transcriptome of Hyriopsis cumingii ventral mantle tissue whose nacre colors were purple and white was sequenced by a new generation of high throughput sequencing technology in order to find candidate genes involved in pearl color produced by H. cumingii. After quality control and assembly, the sequences acquired were blasted against NR, Swiss-Prot, COG, KOG, KEGG, GO and Pfam databases, and then cluster analysis were performed. In total, 72 800 581 bp of clean data, and 89 529 Unigenes were obtained, and 2644 genes were differentially expressed, among which 1323 were up-regulated and 1321 down-regulated. The Unigenes GO function in the transcriptome library was divided into 3 categories: molecular function, cellular component and biological process with 50 branches; it could be divided into 187 classes taking the KEGG database as a reference. Differentially expressed gene analysis revealed that some genes were related to pigment biosynthesis (such as xanthommatin, melanin and pteridine) and metal ion transportation. And there were 6 cytochrome P450, 3 cytochrome b561 and 1 cytochrome b560 genes. They might play important roles in the formation of pearl color of H. cumingii.