Objective To compare the reliability of genetic analysis by biochemical markers and microsatellite DNA in Mongolia gerbil colonies.Method To analyze 27 biochemical marker loci and 13 microsatellite DNA loci of two Mongolia gerbil colonies and compare the results obtained by the two techniques.Result 13 biochemical marker loci of the 27 loci showed polymorphism in the whole population,and the polymorphism rate was 48.1%.11 microsatellite DNA loci were polymorphic in the whole population,and the polymorphism rate was 84.6%.The average effective allelic number derived from biochemical marker analysis was similar to that from microsatellite DNA analysis.Percentage of polymorphic loci and average homozygosity of microsatellite DNA were higher than those obtained by biochemistry marker analysis.But the results of biochemistry marker and microsatellite DNA analyses were coincident in genetic diversity and Hardy-Weinberg equilibrium.Conclusion Both biochemistry maker and microsatellite DNA marker analyses are good methods for analyzing the population genetics of Mongolia gerbil colonies.