Tarter buckwheat (Fagopyrum tataricum Gaertn, Polygonaceae) is a crop of dietary benefits beause of their active component rutin along with other nutritional components. In ancient time it was underutilized crop but at the present time tarter buckwheat must be further evaluated for its contribution to diversifying cropping systems, enhancing human nutrition, and contributing to National economies. Detection and analysis of genetic variation can help us to understand the molecular basis of various biological phenomena in plants. Since the entire plant kingdom cannot be covered under sequencing projects, molecular markers and their correlation to phenotypes provide us with requisite landmarks for elucidation of genetic variation. Genetic or DNA based marker techniques such as RFLP (restriction fragment length polymorphism), RAPD (random amplified polymorphic DNA), SSR (simple sequence repeats) and AFLP (amplified fragment length polymorphism) are routinely being used in ecological, evolutionary, taxonomical, phylogenic and genetic studies of plant sciences.