Abstract: Single nucleotide polymorphisms (SNPs) distribute numerously and high-density throughout the rice genome and are stable in genetics. Several routes have been used for discover SNPs in rice such as sequencing directly to the PCR products of the DNA samples, screening SNPs in the SSR areas and search for SNPs through the rice genome sequences . several genotyping systems have been developed to identify SNPs in the rice genome. High automation in the SNPs identification has become a very convenient operation by the automatized systems. SNP has showed the huge potential in the establishing in the rice genetic maps, genes cloning and functional genomics, MAS in rice breeding and studying in classification and evolution of germplasm.