In the current status there is no explicit demarcation methodology on finding of substitutes (Pratinidhi Dravya). Thus here an attempt has been made to find out substitute by DNA fingerprinting on the basis of similarity and dissimilarity. In this study two samples Alysicarpus longifolius W. & A.Prodr.- Fabaceae, Desmodium laxiflorum DC i.e. of same family, same genus with different species were subjected to fingerprints. In this data we find a more similarities characteristics in both the plants i.e. up to 63%. As per the knowledge of research scientist this is a first moral attempt which throwing lights on concept of Pratinidhi Dravya (Substitution) in Ayurvedic science.