Persian walnut (Juglans regia L.), is very auspicious plant species of Iran from both economical and food points of views. Both wildly grown as well as cultivated forms of this plant species are scattered in different geographical regions of the country and are a valuable source for edible nut as well as job employment. Scattered published data on genetic diversity of this important plant species are mainly based on different molecular data analyses; therefore a meta-analysis of the same cultivars based on several different molecular markers including DNA-sequences and multi-locus markers was conducted to provide a detailed insight on genetic structure of walnuts. The results indicated a moderated genetic variability of about 40 percent in the studied cultivars; however these cultivars are genetically differentiated as revealed by Fst and AMOVA. HGT analyses revealed that the cultivars phylogeny differs to some degree by different markers and therefore a heat map was constructed to reveal the cultivars relationships based on combined molecular data. A higher Pst value was obtained compared to that of Fst genetic differentiation, therefore, it seems that local adaptation and selection have played role in the walnut cultivars’ morphological divergence. LFMM analysis identified some adaptive multi-locus alleles in the studied walnut cultivars.