AbstractSingle nucleotide polymorphisms (SNPs) are an abundant form of DNA variation which have a frequency of 1% or more throughout the genomes. SNPs consist of a single nucleotide base alteration including transition and transversion. They are stable and reliable mutation and are frequently referred to as bi-allelic makers. SNPs can be used conveniently for large-scale and high throughput genome analysis, in particular combining DNA chips and microarrays techniques. Therefore, SNPs provide a novel molecular marker system potentially useful for a wide range of biological disciplines. Here we briefly introduce the history and developments of SNP techniques, including its basic concept, its discovery and screening. We also discuss its applications in different research areas such as genetic mapping in mode animals and plants, DNA fingerprinting and its application in variety identification, species origin and relationship, linkage disequilibrium and associate analysis, and its application in population genetics. We anticipate that SNP markers will contribute greatly to the studies on population genetics, molecular breeding as well as evolutionary biology.