The multimammate rat M. coucha is the most widespread strain to be introduced in biomedical research and various stocks of this strain are maintained in laboratories across the globe. It is an ideal carrier of normally non-human disease to the domestic environment. In order to analyze genetic purity, strains of M. coucha were subjected to PCR-based DNA fingerprinting using sequence tagged microsatellite markers to evolve molecular signature to them. For this, 10 rats sequenced tagged microsatellite markers were used to investigate for their applicability of cross-species amplification in the genome of M. coucha. Out of 10 microsatellite primers tested, four (40%) microsatellite primer pairs [Carboxypeptidase B (CBP), Calmodulin (CALM3), Cell surface protein (CSPMO2) and Insulin like growth factor-I (IGF-1)] could be amplified successfully with exact with product size of 159, 145, 186 and 203 bps respectively in rat. The results suggest that since the above mentioned microsatellite primers get amplified successfully in M. coucha, they may be useful for genetic characterization, evaluation, strain improvement and biomedical research.