Objective To screen for, and identify more-effective microsatellite loci for genetic quality analysisand enrichment of the genetic data in Mongolian gerbils using genomics. Methods Altogether, 357 repetitive sequences inaccordance with the microsatellite criteria were selected from whole-genome sequencing data of Mongolian gerbils. Thecorresponding primers were designed and synthesized based on the flanking sequences of each locus. The genomic DNA ofthe Mongolian gerbils was extracted and polymerase chain reaction (PCR)-amplified with their corresponding primers. Afteroptimizing the primer sequences, the PCR condition, and the gel electrophoresis experiments, the most efficient loci forsuccessful amplification were verified and optimized in various inbred lines and an outbred group of Mongolian gerbils. Theloci were also screened to identify those suitable for genetic quality analysis. Results Among the 357 microsatellitesequences, 135 loci primers were successfully amplified with the PCR product. Ten of them could be used to distinguish twoinbred strains of Mongolian gerbils, including the cerebral ischemia model and the diabetes model. Also, 12 gerbils fromthe outbred group had 23 loci that exhibited polymorphism. Conclusions In all, 135 microsatellite loci of gerbils aresuccessfully screened, some of which can be used for genetic quality analysis in both inbred and outbred groups of Mongolian gerbils.