Microsatellite markers are most valuable tools for characterization of plant genetic resources or population genetic analysis. Since they are codominant and allelic markers, utilizing them in polyploid species remained doubtful. In such cases, microsatellite markers are usually analyzed by treating them as dominant marker. In the current study, it has been showed that despite of losing the advantage of co-dominance, microsatellite markers are still powerful tool for genotyping of polyploid species because of availability of large number of reproducible alleles per locus. It has been studied by genotyping of nineteen sub populations of