The data set contains data used to plot the figures in the article "Genetic diversity and population structure of wheat landraces in the Southern Winter Wheat Region of China." The genotypic file "Geno_data" shows 2023 wheat landrace accessions genotyped with the 15K Axiom Wheat Breeder Genotyping Array (China Golden Marker Biotechnology Co., Ltd., Beijing) according to the manufacturer's guidelines. Quality filtration was conducted on the markers using PLINK v1.07. Quality filtration was performed on the markers using PLINK v1.07. Minor allele frequency (MAF) less than 5% (--maf 0.05), individuals with more than 20% missing SNP calls (--mind 0.2) and markers with more than 5% missing data (--geno 0.05) were considered for filtration. Finally, 7,926 SNP markers and 2,023 genotypes were further analyzed, including population structure, kinship, PCA analysis and genetic diversity analysis.