Abstract: Perilla frutescens（L.）Britt.is an economically and medicinally important species that is officially listed as both food and medicine in China. However, long-standing land-race admixture and poorly defined genetic backgrounds have severely hindered the mining and utilization of superior germplasm.Materials and MethodsTo systematically characterize the genetic-diversity landscape of Chinese perilla germplasm, 70 representative accessions collected from 12 provinces were analyzed. The panel covers the main northern production area（Liaoning, Heilongjiang, etc.; 56 accessions, 80.0%）and representative southern production sites（Yunnan, Anhui, Jiangxi, etc.; 14 accessions, 20.0%）. Hyper-seq, a reduced-representation genome sequencing strategy, was applied for genome-wide scanning for the first time in perilla（Perilla frutescens（L.）Britt.）. A total of 1,918,357 high-quality single nucleotide polymorphisms（SNPs）and 766,430 insertion-deletion（InDel）markers were identified in 20 chromosomes, with an average of approximately 95,918 SNPs and 38,322 InDels per chromosome. Variants were primarily distributed in intergenic regions（69.16%）, with 237,564 variant sites identified in exonic regions. Consensus results from NJ tree, PCA, and ADMIXTURE analyses indicated that the 70 accessions could be divided into four major genetic subpopulations:the Shanxi-Inner Mongolia-Liaoning Inland Group（n=25）,Liaodong Coastal and Eastern Mountain Group（n=13）, the Heilongjiang Group（n=8）, and the Central-Southwest China Group（n=24）, with population structure highly correlated with eco-geographical origin. Overall Nei's genetic diversity index was approximately 0.63, with nucleotide diversity（Pi）values of 0.39 and 0.34 for core and retained germplasm, respectively. Observed heterozygosity（Ho）was slightly lower than expected heterozygosity（He）, suggesting structural differentiation in allele frequencies. A core collection of 18 accessions screened by Genocore covered over 90% of the total genotypic variation. Our results reveal a clear regional differentiation and diversity pattern in Chinese perilla germplasm. Two novel genetic sub-groups—"Liaodong Coastal and Eastern Mountain Group" and "the Heilongjiang Group"—are reported here. The unique genetic status of Yunnan perilla is also highlighted. The generated genomic resources provide a solid foundation for germplasm development, molecular-marker-assisted identification and resource utilization of perilla in different eco-geographic regions, and will facilitate both sustainable industrial development and on-farm conservation of genetic diversity in perilla.