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By using 16 simple sequence repeat (SSR) markers, the genetic relatedness of 21 exceptional walnut genotypes was assessed. A significant degree of genetic diversity was observed within a given population, as indicated by the number of alleles per locus ranging from 2 to 4. WGA-1, WGA-4, and WGA-79 contained the greatest number of alleles (4), followed by WGA-118, WGA-202, and WGA-42. Conversely, WGA-27, WGA-69, and WGA-32 contained the fewest alleles. The range of the PIC value was 0.11 to 0.38. Using model-based cluster analysis, all genotypes were categorized into two primary clusters according to the UPGMA dendrogram, with varying degrees of sub-clustering. All the genotypes were categorized into six genetically distant subpopulations. The genotypes were genetically distinct but had variable degrees of admixture. The anticipated heterozygosity at a specific locus ranged from 0.563 to 0.741. Additionally, population differentiation (Fst) ranged between 0.176 and 0.261. These findings highlight the importance of considering germplasm diversity in walnut breeding programs and conservation efforts aimed at enhancing walnut cultivation in the region. Overall, this study contributes to our understanding of walnut genetic diversity in the Northwestern Himalayan region of Jammu and Kashmir and informs future breeding and conservation strategies.