Conducting DNA fingerprinting of rice germplasm resources and assigning uniform identity information to each germplasm are of great significance for identifying the resource family in China, assessing the genetic basis of resources, improving resource utilization efficiency and protecting the intellectual property rights of the seed industry in rice. In this study, using 5374 rice accessions that had completed whole-genome DNA resequencing as the basis, two sets of whole-genome DNA fingerprinting standards for rice germplasm resources were established through the selection of reference sample resources, analysis of high-quality SNP loci, and selection of the optimal number of SNPs and SNP combinations. Through principal component analysis and phylogenetic tree analysis, the SNPs selected by fingerprinting standards 1 and 2 could represent 94,197 high-quality population common SNPs for population genetic diversity detection. In addition, population genetic similarity analysis verified the effectiveness of fingerprinting standards 1 and 2 for conducting genetic similarity identification of rice germplasm resources. This study is expected to provide technical support for the conservation and utilization of rice germplasm resources and the protection of intellectual property rights in the seed industry, and to provide reference for the development of whole-gene DNA fingerprinting standards for other crops.