Walnuts are a source of benefi cial nutrients (fatty acids, vitamins, phenolic compounds) and are high in calories. In the breeding of this cultivated plant, one of the key areas is selection for fruit quality. A modern cultivar must meet the standards of fruit appearance (large fruit, light kernel color, round shape, easy shell-kernel separation). The study of the genetic structure of walnut collections using microsatellite markers is no less relevant. The article aims to comprehensively evaluate the economically valuable traits of fruits and analyze the genetic diversity of promising elite walnut forms bred by the North Caucasian Federal Scientific Center of Horticulture, Viticulture, and Winemaking employing microsatellite DNA markers. Morphological fruit evaluation was carried out according to 13 traits. The biochemical analysis included total fat content, phenolic compounds, macronutrients (Na, K, Mg, Ca), and water-soluble solids. The molecular genetic analysis was performed using eight SSR markers: WGA001, WGA069, WGA376, WGA276, WGA009, WGA202, WGA089, WGA321. The comprehensive phenotypic and biochemical evaluation of fruits resulted in the identifi cation of elite forms superior to the check cultivar. For these elite forms, the fruit weight was 17-1-18 (13.36 g), MP-82 (14.80 g), YaB-18 (13.47 g); the kernel content was 17-2-23 (61.24 %), 17-5-5 (58.49 %), 17-2-16 (57.7 %); the fat content – MP-34 (68 %), 17-1-18 (61 %), 17-2-16 (62 %), MP-39 (60 %), YaB-5 (60 %). The microsatellite analysis revealed an average allele value per locus of 7.13, which indicates a high level of genetic heterogeneity in the studied sample of elite forms. Using the UPGMA clustering method and PCoA analysis, we revealed the presence of two genetically distinct groups. Th e first one includes large-fruited samples that exceed the check cultivar in terms of fruit weight (MP-82, YaB-18). In the second group, high-oil-bearing forms with a large percentage of kernel yield (17-1-18, YaB-5, 17-2-23, 17-2-16, MP-39, MP-34, 17-5-5) and forms with good shell-kernel separation (17-2-5, 17-2-16, 17-5-5, 17-5-10, MP-39, MP-67, MP-69, MP-170) predominated. Th us, it can be concluded that crossing genetically distant forms is promising not only for solving breeding issues, but also for preserving and increasing the genetic heterogeneity of the breeding walnut gene pool.