Abstract: AIMTo analyze sequences of the nuclear ribosomal RNA small subunit (18S rRNA) gene and the chloroplast matK gene of crude drug Patchouli (Pogostemon cablin) in order to provide molecular evidence for identification of Patchouli drug. METHODSTo sequence the entire 18S rRNA gene and partial matK gene of Patchouli from Guangzhou and its substitute Wrinkled Gianthyssop (Agastache rugosa) from Sichuan using PCR direct sequencing and to detect the homology of two gene sequences between these two crude drugs. RESULTSThe complete 18S rRNA gene sequence is 1 805 bp in length for Patchouli from Guangzhou whereas 1 794 bp for Wrinkled Gianthyssop from Sichuan. The 3′-end sequence of matK gene is 521 bp (747～1 268 nt from upstream of matK gene) for these two crude drugs. Based on multiple sequence alignment, it is found that there are 18 variable sites and 11 aligned gap sites in 18S rRNA sequence, 49 variable sites in 3′-matK sequence between these two crude drugs. The homology is 98.4% for 18S rRNA and 90.6% for 3′-matK between two crude drugs, respectively. CONCLUSIONDNA sequencing can provide an accurate and reliable tool in the crude drug identification of Patchouli and its substitute Wrinkled Gianthyssop.