Objective To establish a rapid SNP(single-nucleotide polymorphism)genetic identification method for the frozen samples, such as frozen embryos and sperm of inbred mice. Methods In this study, the frozen embryos and sperm of inbred mice were provided by Shanghai Lab. Animal Research Center. Whole genome amplification and PCR-LDR genotyping system were used to get the rich DNA sample. Forty-five SNP were genotyped by multiple polymerase chain reaction and ligase detection reaction(PCR-LDR). Results The electrophoresis results showed that the whole genome amplification technique could highly increase the total DNA of frozen embryos. PCR-LDR typing method was suitable for the mouse genome typing of 45 SNPs.Ten strains of inbred frozen embryos and sperms of C57BL/6, BALB/c, FVB/NJ mice were genotyping identified, and their SNP loci data obtained by PCR-LDR were as the same as those of database.The number of frozen mouse embryos was proportional to the number of SNPs detected, and when the embryo number reached more than 12, the detection rate of SNP was 100%.Conclusions This method can be used to the genetic quality identification, and rapidly identify the inbreed frozen mouse embryos and sperms.