The genetic diversity and genetic structure of Petrocosmea qinlingensis artificial breeding population and wild population were analyzed with 24 SCoT primers， This study is of scientific significance to analyze the endangered mechanism of the P. qinlingensis and to formulate population protection and restoration strategies. The results showed that: (1) the average of observed number of alleles, effective number of alleles, Neis gene diversity and Shannon information index of 60 P. qinlingensis test samples were 1.51, 1.31, 0.230 5 and 0.370 3, respectively. This indicates that the genetic diversity of the test material population was low. (2) The analysis results of genetic distance and similarity coefficient among populations showed that the genetic similarity coefficient between 60 test materials of the three populations was 0.955 1 to 0.970 5, and the average similarity coefficient was 0.963 4, which further explained that the genetic similarity among populations was extremely high. Therefore, the genetic background was narrow. (3) The results of molecular variance analysis of P. qinlingensis population showed that 15% of the variation was from among populations, and 85% of the variation was from within population. The comprehensive analysis showed that the genetic diversity of the P. qinlingensis was low in various groups and between populations, and the genetic background was narrow. This may also be one of the important reasons for its poor ability to adapt to the environment, leading to its endangerment.