In this study, we investigated the fingerprint and genetic diversity of Sichuan elite Juglans regia cultivars to improve the identification ability for cultivars. The SSR markers were applied for genetic diversity and cluster analysis of 29 elite J. regia cultivars. The results showed that：（1） 121 genotypes and 80 alleles were identified by the 11 SSR markers, and per primer pair has 7.273 alleles and 11 genotypes. （2） Mean effective allele number (N_e), heterozygosity (H_o), expected heterozygosity (H_e), shannons index (I) and polymorphic information contents (PIC) of the 11 SSR markers were 3.644, 0.645, 0.718, 1.518 and 0.680, respectively. （3） The fingerprint of 29 J. regia cultivars were constructed by primer combination method using primers wga001, wga032 and zmz02. （4） Cluster analysis showed that the 29 J. regia cultivars were classified according to the priority of variety type. There is no obvious correlation among cluster relationship and geographical origin of the local J. regia cultivars in Sichuan. The results suggested that the 11 SSR markers can be applied to analyze the genetic diversity of walnut varieties in Sichuan (PIC>0.5); the genetic relationship of 29 Sichuan J. regia cultivars was relatively close, and theirs genetic basis are relatively narrow.