Objective BALB/ c mutant curly mice and normal BALB/ c mice were genetically detected by microsatellite DNA marker analysis to detect the differential microsatellite loci between BALB/ c mutant curly mice and normal mice. Methods 38 microsatellite DNA loci were selected and their variation in the BALB/ c mutant curly mice, BALB/ c mutant hairless mice and normal BALB/ c mice were detected by multiplex fluorescence PCR and STR scanning genotyping. Results There were 27 the same microsatellite loci between the 38 microsatellite loci in BALB/ c mutant curly mice and normal mice, and there were 11 differential loci, with a mutation rate of 28. 9% (11/38). There were 30 the same sites between BABL/ c mutant hairless mice and normal mice, and there were 8 different loci, with a mutation rate of 21.1% (8/38). There were also 12 differential loci between BABL/ c mutant curly mice and hairless mice. Conclusions BALB/ c mutant curly mice have a higher mutation rate and are significantly higher than those of hairless mice, demonstrating that the mutations in curly mice and hairless mice are two completely different mutations. These results provide reliable theoretical data for the future study and development of BALB/ c mutant curly mice.