In the current study, significant variations were identified for seven fruit traits of the walnut accessions. The highest correlations were detected between nut height and nut width, and between nut weight and kernel weight. Most traits had a continuous normal binominal distribution. A total of 16,774 single-nucleotide polymorphism (SNP) markers based on diversity arrays technology were generated and after filtering the missing data, the remaining 13,611 SNP data were used for genotyping. STRUCTURE (v.2.2) analysis revealed two possible scenarios (K = 3 and K = 5) according to the results of AK computation. While K = 3 indicated that walnut cultivars were clustered into three different groups, K = 5 revealed five different groups. Results of the dendrogram tree analysis were supported by the results presented in the STRUCTURE analysis. A total of 98 association signals were detected with FDR <= 0.05 from MLM (K) using BLUP predictors for the seven agronomic traits. Out of these 98 associations, seven SNPs were associated with nut weight, 26 SNPs with nut length, 15 SNPs with nut height, 18 SNPs with nut width, 18 SNPs with shell thickness, 12 SNPs with kernel weight, and 2 SNPs with kernel ratio.