In the present study, we conducted a detailed analysis of the genetic diversity and structural organization of 96 domestic Korean rice varieties (Oryza sativa L.) using 2,565 high-resolution TCS-based single nucleotide polymorphism (SNP) markers. Genetic structural variations were investigated using diversity indices, PCA, genetic similarity, and network analysis. Genetic diversity analysis revealed a significant expansion of the genetic foundation after the 1980s, marked by a sharp increase in the number of alleles (Na) from the 2000s. Despite this, high genetic homogeneity was maintained, with an average similarity of 77.7%. The observed 10% difference among same-cross varieties suggests that critical genetic variations are fixed by strong selection pressures for quality traits. Network analysis (85% similarity threshold) confirmed that the Korean rice breeding population followed a distinct core-periphery model (eight communities). The connected 84 varieties had a centrality range of 0.01 0.39. Core Variety Groups (e.g., ‘Junam’ and ‘Sindongjin’) exhibited the highest centrality (up to 0.39), indicating their extensive use as key breeding parents and their function as the central axis of the genetic network. Bridge Variety Groups (e.g., ‘Hwayeong’ and ‘Samkwang’) played an intermediary role linking clusters. Crucially, 12 ‘isolated accessions’ showed zero centrality (0.00), representing a genetic disconnect from the main pool. This quantitative network-based assessment provides essential fundamental data for breeders to select appropriate germplasms. Furthermore, the findings suggest that the current cultivar naming system, which inadequately reflects genetic relationships, requires reassessment, and that the establishment of objective management standards based on this research is warranted.