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Genotype specific fingerprints were detected in two grain amaranthus varieties KBGA1 and Suvarna using SSR and RAPD markers. In this study 41 Pigeon Pea SSR markers and 6 RAPD markers were used to generate DNA fingerprints for the two varieties of grain amaranthus. Analysis of polymorphic fragments generated from SSR and RAPD markers revealed the genetic variation between grain amaranthus varieties KBGA1 and Suvarna. The results indicate that DNA markers are appropriate tools for assessing genetic variation within and between the species of amaranthus and suggest that cultivated varieties of Amaranthus have significant genetic variation. The differences generated by the markers can be used as fingerprints for detecting the varieties. This is the first report of the utilization of legume microsatellite markers in Amaranthus.