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High-throughput genomic technologies are enabling the identification of thousands or even millions of single-nucleotide polymorphisms (SNPs). SNP markers are frequently used to analyze crop varieties, with the marker data summarized in a common VCF file. At present, it is difficult to identify the minimal SNP set, the smallest sets that can distinguish between all crop varieties listed in a VCF file, due to the absence of available ready-to-use tools capable of such characterization. Here, we describe the development of the ready-to-use open-source tool MDSearch (Minimal Discriminatory SNP Set Search) based on the identification of the MDS (minimal discriminatory set) of SNPs using random walking staring from the maximal discriminatory set. MDSearch can be used for disploid as well as poliploid species and both phased and unphased VCF files. MDSearch has been validated using a publicly available dataset of barley SNPs obtained by genotyping-by-sequencing. As a result, we have successfully identified a discriminating set of 19 SNP markers capable of distinguishing all 254 barley varieties included in our study. We expect that this program will prove useful to genomics researchers to support a variety of certifications.