Abstract: In this study, Illumina HiSeqTM2000 high-throughput sequencing technology was employed to perform transcriptomes of linalool- and hetero-type camphor leaves. Classification, functional annotations and Pathway annotations were performed using GO, Nr, Nt, Pfam, KOG, Swiss-prot and KEGG databases. The results indicate that a total of 34.45 GB clean data was generated from 2 chemotypes of camphor leaves, and assembled into 312 457 Unigenes. Among them, 11 685 Unigenes were identified to be differentially expression in linalool- and hetero-type camphor leaves, including 6 481 up-regulated and 5 204 down-regulated Unigenes; 39 genes encoding proteins involved in terpene synthases, including 6 monoterpene biosynthesis, 7 diterpene biosynthesis, 12 sesquiterpene and triterpene biosynthesis, and 14 terpene skeleton synthesis. Three monoterpene synthase genes TPS14 were down-regulated in linalool-type compared to the hetero-type, and their expression were verified using transcriptome FPKM and q−PCR. A total of 134 851 SSR sites were detected from 88 016 Unigenes, including 103 478 Unigenes at single SSR sites and 31 373 Unigenes containing 2 and more SSR sites.