Abstract: 【Objective】 ISSR markers were used to study the genetic diversity and genetic structure in order to provide a theoretical basis and technical support for appropriate conservation and application of existing genetic resources of walnut. 【Method】 Genetic relationship of 5 populations and 1 type (163 walnut samples) walnut was analyzed using ISSR markers.【Result】 117 bands were amplified by 13 informative and reliable primers, of which 98 were polymorphic loci. At species level, the percentage of polymorphic loci (PPL) was 83.76%, Nei’s gene diversity (H) was equaled to 0.3010, Shannon’s Information index (I) was 0.4182. At population level, the average value of PPL was 68.36%, the mean value of H amounted to 0.1265, the general average of I was 0.1651. Genetic coefficient of differentiation (Gst) among populations based Nei’s gene diversity was equaled to 0.6425, which showed 64.25% genetic variation existed among populations. The mean value of Nei’s genetic identity was equaled to 0.7499, estimation of gene flow from Gst (Nm) was 0.2782, which was able to be considered that gene flow was blocked among 6 populations and types, this result was uniform with that obtained by using Nei’s gene diversity. Analysis of AMOVA also showed genetic variance among populations was larger than within a population. Mantel test and UPGMA dendrogram based Nei’s genetic distance showed that genetic distance among populations had more significant correlation with geographic distance. 【Conclusion】The walnut germplasms in Xinjiang have a high level of genetic diversity, and the genetic differentiation is also larger. Germplasm protection and exploitation strategies of Amygdalus ledebouriana Schlecht should be prior to conduct in situ conservation, and by monitoring the level of genetic diversity to evaluate the effectiveness of its protection.

Key words: Juglans regia L , germplasms resources , genetic diversity , ISSR