Pogostemon cablin (Blanco) Benth. is an important medicinal plant; however, its molecular biology remains largely unexplored. Here, we report the results of whole transcriptome-wide analyses of P. cablin using next-generation sequencing technology. In the present study, we generated 108,996 unigenes using RNA sequencing data. Among these unigenes, 65,536 were annotated in the NR database. There were 40,670 intact open reading frames (ORFs), which accounted for 69 % of the 58,820 predicted ORFs, demonstrating that our assembled transcriptome was of high quality. Gene expression levels in the leaf and stem were quantified, and 18,481 unigenes (17 %) were determined to be significantly differentially expressed. The patchouli alcohol (PA) and pogostone (PO) metabolic pathway of P. cablin was also reconstructed, and among the 17 putative homologs to PA and PO biosynthesis-related genes, seven were significantly upregulated in the stems, and three genes were significantly upregulated in the leaves. The correlation between the essential oil contents of P. cablin and the potentially pivotal genes for PA and PO production were identified. Considering that the contents of PA and PO in leaves and stems are markedly different in the same plant and we did not detect any pattern in the expression levels of candidate genes between leaves and stems, we speculate that after the biosynthesis, more PA probably accumulates in the leaves, and more PO in the stems of P. cablin. The transcriptome of P. cabin will facilitate further researches on the molecular system biology of the Pogostemon genus, as well as the in-depth studyies of PA and PO biosynthesis and its potential applications for genetic engineering.