Objective To screen out single nucleotide polymorphisms (SNPs) that can be used to rapidly identify four common strains (Wistar, GK, BN, and SD) of rats and verify their reliability. Methods First, whole genome resequencing was performed on Wistar and GK rats. Using bioinformatic techniques to align the resequencing reads to the BN rat reference genome to detect specific SNPs within the genome of Wistar and GK rats, we selected a group of candidate SNPs. Then, we used Sanger sequencing and the DNA pooling method to screen and validate the candidate SNPs in four strains of rats. Results 94 800 and 106 019 homozygous-specific SNPs were detected in the Wistar and GK rats,respectively, of which 56 216 were shared by Wistar and GK rats. Only 38 SNPs were found to show different genotypes among BN, Wistar, and GK rat reference genomes, of which 15 were selected as candidate SNPs. Finally, 13 SNPs were screened, and the genotype of each locus in the four strains of rats was identified. Conclusions Thirteen SNP markers were identified and validated. These SNP markers can be used to rapidly distinguish Wistar, GK, BN, and SD rats.