In order to provide a theoretical basis for the sustainable in-situ conservation and innovative utilization of wild jujube resources in Ningxia, four representative wild jujube populations in different ecological sites in Ningxia were selected to analyze the genetic diversity in Ningxia on the basis of the field survey, in which 30 trees were randomly selected from the four wild jujube populations, and the leaves were collected. A novel genomic and molecular marker SNP（single nucleotide polymorphism）technique was used, and the genetic structure and evolutionary relationship of the four wild jujubes from Ningxia were revealed on the molecular level. The main research results were as follows. The genetic characteristics of wild jujube populations in Ningxia were evaluated by SNP markers, and the geographical distribution could be divided into two main geographical groups, which represented the central and northern regions of Ningxia, respectively. The central region included Wuzhong Hongsibao population, and the northern region included Zhongwei Rizhaoshan population, Lingwu Baijitan population and Helanshan Gunzhongkou population. The genetic relationship between the wild jujubes populations was that Helanshan Gunzhongkou population was more similar to Lingwu Baijitan population, while Zhongwei Rizhaoshan population and Wuzhong Hongsipu population were separated into a single group. The genetic differentiation degrees of Zhongwei Rizhaoshan population and Lingwu Baijitan population were the highest, with the Fst of 0.191; the lowest degree of differentiation was Helanshan Gunzhongkou population and Lingwu Baijitan population, with the Fst of 0.084, belonging to medium differentiation.