Objective To analyze the genetic quality of domestic 24 inbred strains mice using microsatellite loci panel. Methods Previously selected 30 microsatellite loci of mouse with high polymorphism and more allele numbers were used and the corresponding primers labled with flurocence were synthesized. Then the genomic DNA samples of each mouse were amplified by PCR and the products were analyzed by STR scanning to genotype for each inbred strain. Results Of total 24 inbred strains, 15 inbred strains showed same genotype results within one strain at 30 loci. Among different strains, microsatellite loci indicated polymorphism which could be used to distinguish different strains. However, the rest 9 strains demonstrated polymorphism within strains. Conclusions It offered an useful microsatellite panel to detect genetic quality of inbred mice and distinguish different strains with the optimized microsatellite loci.