Abstract: Molecular identifications of Lobelia chinensis and Mazus pumilus, as well as a specific PCR rapid method based on the SNP in rbcL sequence to differentiate between the two rather similar Chinese medicinal material were establish in this study. Commercial samples of 9 L. chinensis and 7 M. pumilus from different origins were collected to extract total DNA for rbcL gene sequencing. SNPs in the rbcL sequences of the samples were isolated using the ClustulX 2.1 program. The primers for identifying the two material were designed based on the SNP site. A specific PCR method was subsequently developed to rapidly and effectively detect the markers by the addition of SYBR Green I dye.