AimsTo determine the molecular variability and develop specific Sequence Characterized Amplified Region (SCAR) marker for the detection of Magnaporthe grisea causing blast disease in finger millet. Methods and ResultsRandom amplified polymorphic DNA (RAPD) was performed with 14 isolates of M.grisea using 20 random primers. SCAR marker was developed for accurate and specific detection of M.grisea infecting only finger millets. The genetic similarity coefficient within each group and variation between the groups was observed. Among the primers, OPF-08 generated a RAPD polymorphic profile that showed common fragment of 478bp in all the isolates. This fragment was cloned and sequenced. SCAR primers, Mg-SCAR-FP and Mg-SCAR-RP, were designed using sequence of the cloned product. The specificity of the SCAR primers was evaluated using purified DNA from M.grisea isolates from finger millets and other pathogens viz., Pyricularia oryzae, Colletotrichum gloeosporioides, Colletotrichum falcatum and Colletotrichum capcisi infecting different crops. The SCAR primers amplified only specific 460bp fragment from DNA of M.grisea isolates and this fragment was not amplified in other pathogens tested. ConclusionSCAR primers distinguish blast disease of finger millet from rice as there is no amplification in the rice blast pathogen. PCR-based SCAR marker is a convenient tool for specific and rapid detection of M.grisea in finger millets. Significance and Impact of the StudyGenetic diversity in fungal population helps in developing a suitable SCAR marker to identify the blast pathogen at the early stage of infection.