Abstract:In order to understand systematic relationship of Verbenaceae, chloroplast genes, such as ycf6-psbM, trnV-atpE, rbcL, trnL-F, psbM-trnD, atpB-rbcL, trnC-ycf6, trnH-psbA, rpl36-infA-rps8 and nrDNA ITS of Premna microphylla Trucz. were amplified by PCR and sequenced. Among these loci, rbcL, trnL-F and trnHpsbA were efficient for both PCR amplification and DNA sequencing, while other sequences don't conform to DNA barcode standard, ITS had no specific bands, ycf6-psbM could not sequence successfully, and the others had double peaks or high noisy values. However, rbcL is better than others according to DNA barcoding standard. The phylogenetic relationships among four genera from Verbenaceae, such as Premna L., Vitex L., Verbena L., and Clerodendrum L., and four genera from Labiatae, such as Lamium L., Stachys L., Salvia L., and Teucrium L., were studied by both combined and individual analyese using the chloroplast genes rbcL and matK sequences. The gene trees were constructed by maximum parsimony method with Lithospermum multiflorum as outgroup. It suggested that Premna L. and Clerodendrum L. were supposed to be moved to Labiatae from Verbenaceae and Verbena L. in Verbenaceae taxonomically, and the systematic position of Vitex L. was worthy of further study.