Abstract: In order to clarify the genetic background among the different provenances clones of Pinus armandii seed orchard in the Zixi mountain tree farm in Chuxiong City, Yunnan Province. The needles of 97 clones were taken from 6 provenances which was used to extract total DNA by modified CTAB method, and the genetic diversity was analyzed by SCoT molecular markers, to evaluate the germplasm resource. The main findings are as follows: 34 SCoT primers with clear bands and stable reaction were screened from the published SCoT primers in the existing literature. After SCoT-PCR were amplified, the allele number of 6 provenances of P. armandii was 5.2647, Shannon's information index(I) was 1.3786, Nei's gene diversity index(H) was 0.6904. It indicated that the genetic diversity of 6 provenances of P. armandii was high. The genetic distance between provenances in close geographical locations was not always close and were not in one category, and the geographical distance did not have significant influence on its genetic distance. The genetic differentiation coefficient among provenance(G_st) was 0.0541, and the genetic variation was mainly existed within each provenance, it accounted for 94.59% of the total genetic variation. The gene flow in P. armandii population was large(average N_m was 4.3683 > 1). So, high levels of gene flow may weaken genetic differences among various provenance.