ObjrctivePurity of laboratory animals plays a critical role affecting the experimental results. The aim of this study was to validate a high-throughput genotyping platform, valuable in inbred mouse genetic DNA monitoring and strain identification. Methods Multiple polymerase chain reaction and ligase detection reaction (PCR-LDR) genotyping panels were constructed. Forty-five single-nucleotide polymorphism (SNP) on 21 chromosomes were selected as targets, as well as specific primers and probes to these SNP were designed, respectively. A multiple PCR-LDR genotyping protocol was established. ResultsForty-five SNP were successfully genotyped in four panels. The positive detection rate of 3,4 and 45 SNPs were 100%, 90.9% and 36.4%, respectively. All samples collected were homozygous and their genotypes were identified by PCR-LDR. Conclusion The results of this study provide a rapid and high-throughput genotyping approach, which is sufficient for genetic contamination monitoring and strain identification.