The molecular maker system TRAP was utilized to develop a novel more accurate tool to identify the variety and establish the evolutionary relationship of different kind of Salvia miltiorrhiza Bge.  PopGene 32 software was applied to conduct the cluster analysis and genetic dendrogram establishment.  The results showed that 203 different fragments were amplified with 6 pair primers using the TRAP marker system.  The polymorphic fragments number is 43, which takes up to 21.1%.  The cluster analysis shows that the 4 materials we used in this study can be classified into 2 main groups and 3 subgroups.  The genetic identity is 0.078 8 and the average genetic distance is 0.924 5 among the four materials in this study.  A new tool using the TRAP marker system is more accurate and can be used to identify different kind of Salvia miltiorrhiza Bge at molecular level.