In this study, a garlic DNA fingerprinting system based on single nucleotide polymorphisms (SNPs) was developed using representative cultivated garlic accessions. SNP markers were identified based on reduced-representation genome sequencing (GBS) data from 77 garlic accessions. A total of 26,701,817 raw SNPs were detected and subsequently filtered to obtain 7,006 high-quality candidate SNP loci. Among these, KASP primers were successfully designed for 4,297 loci, corresponding to an assay design