Abstract: AIMTo provide molecular evidence for quality evaluation and GAP production of Pogostemon cablin (Blanco) Benth. cultivated in different regions in Guangdong and Hainan provinces, China, by comparing two sequences (1.2 kb of plastid matK gene and 1.8 kb of nuclear 18S rRNA gene) and two chemotypes (Pogostone-type and Patchouliol-type in essential oil composition). METHODSPCR direct sequencing was applied to detemine the matK and 18S rRNA sequences for six samples of Pogostemon cablin from different localities. RESULTSThe matK sequences of six samples of Pogostemon cablin from different regions of cultivation are 1 245 bp in length, which coding 415 amino acids of protein (maturase), and 18S rRNA sequences are 1 803～1 805 bp in size. Based on multiple sequence alignment, there are 47 variable sites in the matK sequence of these six samples, 17 in the 18S rRNA sequence. The cluster tree reconstructed by UPGMA method shows that the sequence divergence both in matK and 18S rRNA genes among six samples of Pogostemon cablin was well correlative with their regions of cultivation and intraspecific chemotypes of essential oil composition. CONCLUSIONCombining with chemical and biogeographical data, DNA sequencing can become a powerful tool in the key technique-species identification of quality evaluation and GAP production of Pogostemon cablin.