SNP (single nucleotide polymorphism), as the latest generation of genetic molecular markers, has been widely accepted in multiple research fields. This article focuses on the exploitation and detection of SNP molecular markers and their application in variety identification in crop species. At present, the exploitation of SNP markers mainly relies on the polymorphisms either released in public databases or generated by high-throughput sequencing. The polymorphisms could be detected with the traditional detection method using gel electrophoresis to new high-throughput automated detection technologies. In crop variety identification, it is recommended to use gene chip or genotyping by sequencing (GBS) technology for crops with large sample populations and multiple SNP detection markers, and for which with small sample populations and few SNP detection markers could more flexible, efficient and lower cost by kompetitive allele specific PCR (KASP) or high resolution melting (HRM) typing technologies.