Abstract: Single nucleotide polymorphisms (SNPs), the DNA polymorphisms generated by single nucleotide variations at genomic level, are the third-generation DNA markers following restriction fragment length polymorphism (RFLP) and simple sequence repeats (SSR). SNPs were originally used in the analysis of the relation between diseases and single nucleotide mutation in human disease studies. With rapid development of detection methods and improvement of relevant databases, SNPs have been extensively used in a wide range of genetic studies including genetic maps construction, population genetics, genetic relationship, association studies and gene function analysis. In this review, the occurrence, characteristics, detection methods and applications of SNPs in genetic studies on marine organisms are summarized, which is expected to better apply SNPs in the genetics-assisted breeding of marine aquaculture animals.