Single nucleotide polymorphism (SNP) sites are widely distributed in plants. SNPs-based markers have become an important molecular tool for crop genetic research due to their high resolution and co-dominant. This study aims to develop SNP molecular markers based on high resolution melting (HRM) technology and to estimate their genotyping efficiency between cultivated rice and wild rice, providing a reliable, simple and rapid tool for gene discovery, variety identification and molecular breeding in rice in the future. Genome-wide scanning of SNPs were performed between the cultivar Huanghuazhan and wild rice Oryza rufipogon Griff. Y605 using the rice 9K SNP microarray. Then we selected and developed HRM technology-based specific molecular markers from these SNPs. These molecular markers were subsequently used for genotyping of BC3 backcrossed populations with their parents Huanghuazhan and Oryza rufipogon Griff. Y605 to verify their validity. A total of 4,198 SNPs were found between Huanghuazhan and wild rice Y605 by the rice genome 9K SNP microarray, almost evenly distributed on all the chromosomes. Then 5 SNPs were randomly selected from the first, chromosome to develop HRM technology-based specific molecular markers. These markers were accurate and efficient in genotypeing of BC3F1 and BC3F2 populations of Huanghuazhan and wild rice Y605, as well as the homozygous parents and F1 heterozygous. In addition, the wild rice fragments was detected in the ZY1-1~ZY1-4 marker interval of the first chromosome of the backcross. The genome-wide rice 9K SNP microarray can be well applied to the development of SNP markers in rice. The developed specific SNP markers can be accurately and efficiently utilized in genotyping cultivated rice and wild rice. Further development of genome-wide rice SNP markers based on HRM technology will provide an efficient molecular detection tool for molecular genetic research, favorable genes discovery and breeding applications of wild rice.