A total of four microsatellite markers were used across two hybrids and 12 rice varieties for theircharacterization and discrimination. SeedDNA isolation protocol has been standardised and the same protocol was for the characterization of thirteen varieties and two hybrids. The popular rice hybrids viz., KRH-2 and KRH- 4 and used a rice microsatellite marker RM206, RM 234, which exhibits genotype specific amplification with respect to KRH2, to check for impurities. The PCR was successful with respect to the DNA isolated from single seeds and also RM 276 and by using this method we can detect the contaminants.