Objective To analyze the genetic quality of 24 domestic inbred strains mice using microsatellite loci panel. Methods Previously selected 30 microsatellite loci of mouse with high polymorphism and more allele numbers were used to synthesize corresponding fluorescently-labeled primers. Then the genomic DNA samples of each mouse were amplified by PCR and the products were analyzed by STR scanning to genotype the inbred strains of mice. Results Out of the 24 inbred strains, 15 inbred strains showed the same genotype 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 Our stuoly provides a useful microsatellite panel to detect genetic quality of inbred mice and distinguish different strains with the optimized microsatellite loci.