In this study, the phenological and genetic diversity of walnut genotypes from open pollination from ‘MR’ with red kernel color was determined. To determine the phenotypic variation in the study, traits such as budburst date, leafing date, leaf yellowing date, and defoliation date were investigated in plant materials. ISSR primers were used to identify genetic differences. It was determined that there was an average variation of 76.61% in the budburst date, 62.32% in leafing date, 67.58% in the leaf yellowing date, and 46.76% in the defoliation date between the main genotype (MR) and progenies. The study also performed PCA analysis. As a result of this analysis, PC1 was determined as 42.30, PC2 as 32.58, PC3 as 18.48, and PC4 as 6.64. These findings explained the phenotypic variation. The molecular examinations revealed that there were 47 bands in total, with the majority of these bands (80.85%) exhibiting polymorphic. Polymorphism Information Content (PIC) value varied between 0.51 and 0.86, while the average number of alleles was calculated to be 7.83. The dendrogram generated based on the UPGMA criteria was bifurcated into two primary clusters, with the genetic similarity ratio spanning from 0.57 to 0.94. As a result of the study, it was determined that the MR walnut genotype and its progenies obtained from open pollination have a significant variation both phenologically and genetically.