This study analyzed genetic background of 52 advanced ‘Dongzao’ (Zizyphus jujuba Mill. cv. Dongzao) trees and their control, ‘Jinsixiaozao’ and ‘Jianzao’ cultivars from Hebei and Shandong provinces using amplified fragment length polymorphism (AFLP) markers with 16 pair of Mse I/EcoR I primer combinations. Cluster analysis was performed by using of unweighted pair group method with arithmatic mean (UPGMA) method based on SM similarity coefficient. The results were as follows: a total of 565 bands were amplified by 16 primer pairs, of which, 225 were the polymorphic bands including ‘Jinsixiaozao’ and ‘Jianzao’ cultivars, 99 were the polymorphic bands among ‘Dongzao’ advanced trees. There was a little difference among the group of ‘Dongzao’ advanced trees (the average similarity coefficient was 0.9792), though the difference was smaller than the difference between ‘Dongzao’ with ‘Jinsixiaozao’ and ‘Jianzao’ cultivars (the similarity coefficient were 0.8294 and 0.7977, respectively). The three cultivars were divided into 3 groups and the group of ‘Dongzao’ advanced trees were divided into several part in the cluster analyzing map. The genetic distance of the old ‘Dongzao’trees and the ‘Dongzao’ advanced trees from Huanghua county, Hebei province were bigger than the ones from Binzhou city, Shandong province, the similarity coefficient were 0.9649 and 0.9946, respectively. But there were some individual candidate of aberrance among the latter. The above-mentioned results showed that there were some variation among ‘Dongzao’ cultivar and the eximious traits of the advanced trees were not all attributed to the different growth condition and cultivating methods. So the results were very helpful to the genetic improvement and the selection of advanced trees of ‘Dongzao’ cultivar.