CDDP molecular marker was used to analysis genetic diversity of 47 Paeonia rockii DNA. The results showed that: (1) the orthogonal experimental design was used to optimize CDDP amplification system on P. rockii resources in primers and template DNA. A suitable CDDP reaction system was established: the CDDP reaction mixture, with a total volume of 20 μL, consisted of 10 μL of 2×Es Taq MasterMix, 1.5 μL of 1.0 pmol/μL primer, 4 μL of 15 ng/μL DNA and 4.5 μL of ddH2O. (2）19 of 21 primers yielded 112 bands, 97 were polymorphic which accounted for 86.61％ of all bands. (3) The results of UPGMA showed that: 47 P. rockii were grouped together with the same color in general. The similarity index value was 0.72~0.95 which showed the similarity degree among 47 P. rockii was high and the difference degree was low. In total, CDDP molecular marker was suitable for analyzing genetic diversity of P. rockii. The emergence of specific bands could provide theoretical basis for further study the identification of P. rockii.