Abstract :【Objective】The purpose of this experiment is to study the genetic diversity of Xinjiang wolfberry germplasm resources at molecular level by SCoT, and established their DNA fingerprints, which will provide some guidance for the Germplasm identification, Breeding of new varieties and Variety improvement.【Methods】The molecular marker technique of SCoT,PopGen32 software and NTSYS-pc2.10e statistical software were used to study the genetic diversity of 26 type and 4 wild varieties in Xinjiang , and the DNA fingerprinting was also established.【Results】A total of 256 bands were produced by 9 SCoT primers, and polymorphic bands were 217 which accounted for 84. 90% in the total amplified fragments.The polymorphism information content(PIC) values of these markers varied from 76.75% to 91.31%，The average value of effective number of alleles,Nei's genetic diversity and Shannon information index were 1.4303,0.2583 and 0.3948. respectively,The genetic similarity coefficient of 30 wolfberry samples ranged from 0.5938 to 0.8398. Based on SCoT molecular markers and the unweighted pari group method with arithmetic average (UPGMA) and Principal coordinate analysis，All samples could be divided into two groups and 4 subgroups accordingly at the GS of 0.65 and 0.72，In addition, the DNA fingerprints of 30 wolfberry samples was constructed by using the 5 SCoT primers，【Conclusion】the genetic diversity of Xinjiang wolfberry germplasm resources was relatively abundant, The results indicated that SCoT marker is suitable for the analysis of genetic diversity and construction of DNA fingerprinting of Xinjiang wolfberry germplasm resources. Moreover, It provides a wealth of genetic basis for Xinjiang Wolfberry Germplasm Resources identification and breeding of new varieties.