Microsatellites are highly polymorphic, so they have been very useful in population genetics studies. High level of allelic variation, co-dominant mode of inheritance and potential for automated analysis make them an excellent tool for a number of approaches like genotyping, mapping, and genetic characterization. The resolution capability of Metaphor agarose gel is very fine. Study was conducted on 50 local pati ducks. Blood sample was collected from 5 different areas of Assam. Presently, a panel of 17 informative duck microsatellite markers were identified from database as reported by Alyethodi and Kumar (2010) and Huang et al. (2005). MAGE was successful in clearly separating the alleles with a size difference of very small difference. In microsatellite analysis for large number of samples MAGE can be considered very economical for analysis of polymorphisms.