Objective To analyze the genetic characteristics of seven frequently-used inbred mouse strains in core colonies from Shanghai suppliers. Methods 48 pairs of microsatellite primers with high polymorphism were screened out and combined into 11 sets of multiplex PCR primer mix labelled with two dyes (FAM and HEX). By these primer mix, the DNA samples of the seven strains were genotyped. The genotyping data were analyzed using statistical software. Results All the 48 microsatellite loci were homozygous for all inbred mice of the seven strains. On each microsatellite locus, the PCR results of the mice in the same population showed monomorphism, and that of the mice in different populations showed polymorphism, whether the populations were of the same strain or not. But the genetic distances between the populations of the same strain were all closer than that of different strains. The phylogenic tree showed that the populations of the same strain were first get into one cluster. The genetic relationship between the strains of C57BL/6 and other six strains were all far. Conclusions Genetic differences exist on 48 microsatellite loci between the core colonies of seven inbred mouse strains from two suppliers in Shanghai.