Abstract: The goal of this study was to investigate the genetic stability of the C57BL/6J (B6) inbred mouse strain maintained in different breeders. Three populations of B6, Pop1 and Pop2 purchased from Beijing and Pop3 purchased from Shanghai, were examined. Fifteen microsatellite loci reported to be polymorphic among inbred strains were amplified using FAM labeled primers and genotyped with ABI Prism 377 automated sequencer. Seven loci were found polymorphic, and all the loci were homozygous in all the three populations. The present study indicates that genetic variation occurs in different B6 populations although they are still inbred in each breeder. The mechanism of genetic variation is not well understood now, but it is very important to know the precise content of the B6 genome before use of this strain in research.