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Background Lycium chinense is well known in traditional Chinese herbal medicine for its medicinal value and composition, which have been widely studied for decades. However, further research on Lycium chinense is limited due to the lack of transcriptome and genomic information. Results The transcriptome of L. chinense was constructed by using an Illumina HiSeq 2000 sequencing platform. All 56,526 unigenes with an average length of 611 nt and an N50 equaling 848 nt were generated from 58,192,350 total raw reads after filtering and assembly. Unigenes were assembled by BLAST similarity searches and annotated with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology identifiers. Using these transcriptome data, the majority of genes that are associated with phenylpropanoid biosynthesis in L. chinense were identified. In addition, phenylpropanoid biosynthesis-related gene expression and compound content in different organs were analyzed. We found that most phenylpropanoid genes were highly expressed in the red fruits, leaves, and flowers. An important phenylpropanoid, chlorogenic acid, was also found to be extremely abundant in leaves. Conclusions Using Illumina sequencing technology, we have identified the function of novel homologous genes that regulate metabolic pathways in Lycium chinense. [ABSTRACT FROM AUTHOR]