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Identification of cultivars is the prerequisite for commercialization of any agricultural plant. Cultivar identification using biochemical and morphological markers is a traditional approach which is influenced by the environmental factors and age leading to inaccurate identification of cultivars. Cultivar identification is a major constraint for plants with high morphological similarity which in turn affects its commercialization. To mitigate this, molecular marker system has been developed and employed for identifying and characterizing the plant varieties or cultivars of interest. The present review deals with the role of different molecular markers in cultivar identification and its current status. Though there are some limitations with the molecular markers, several suitable markers like RAPD, ISSR, SSR, SNP, SCAR, CAPS etc. are present for a wide range of plants. These makers could be efficiently used for authentic identification of plant cultivars. Further, suitable markers need to be developed for authentic identification of other promising cultivars of important plant species.