The invention relates to the technical field of mouse strain identification, and particularly discloses application of an SNP (Single Nucleotide Polymorphism) marker in inbred line mouse strain identification and a primer sequence. Specifically, according to the application of the SNP marker in inbred line mouse strain identification, the SNP marker comprises 15 SNP loci; the inbred line mouse strain is selected from the group consisting of C57BL / 6J, C57BL / 6N, BALB / c, FVB, DBA / 2, CBAA / CaJ and C3H. The invention also discloses an application of the primer sequence for synthesizing the SNP site in inbred line mouse strain identification. According to the application, seven inbred line mouse strains of C57BL / 6J, C57BL / 6N, BALB / c, FVB, DBA / 2, CBAA / CaJ and C3H can be identified at the same time, and the accuracy of inbred line mouse strain identification results is improved.