To clarify the genetic diversity characteristics of dominant rice varieties in Jilin Province, this study used 66 dominant rice varieties approved in Jilin from 2020 to 2025 as experimental materials. By combining whole-genome 1.5K SNP chip technology with systematic agronomic trait evaluation, we systematically analyzed their genetic diversity level, japonica indica index, functional gene genotypes, and phenotypic traits. The results showed that a total of 3 703 valid SNP loci were detected using the 1.5K SNP chip, of which polymorphic loci accounted for 47.15%. The mean values of the gene diversity index (GD) and polymorphism information content (PIC) were 0.183 and 0.152, respectively, indicating a relatively low level of polymorphism and a narrow genetic base. Analysis of japonica-indica lineage revealed that the japonica indica index of all varieties ranged from 0.770 to 1.000, with an average of 0.914, showing a typical japonica genetic background, while only a few varieties contained a small proportion of indica lineage. Functional gene analysis found that the tested varieties generally lacked favorable alleles of disease resistance genes such as Pi65, cold tolerance genes such as qCTB7, and quality-related genes such as Chalk5. Cluster analysis divided the 66 varieties into three groups, reflecting a genetic structure characterized by both intra-unit clustering and inter-unit mixed clustering. In terms of agronomic traits, recent dominant varieties have not achieved significant breakthroughs in yield or grain shape, and the proportion of late-maturing varieties has shown a downward trend. The findings of this study provide a scientific basis for optimizing and adjusting the direction of rice variety breeding in Jilin Province.