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The hybrid rice, due to its higher productivity has been anticipated to play a key role in global food security. But, high level of genetic purity of hybrid seed is essential to exploit the moderate level of heterosis observed in this crop. Conventionally, the genetic purity of rice hybrids is assessed by the grow out test (GOT). Being land and labor intensive, time consuming and influenced by the environment, there is an immense need to replace GOT with a simple, rapid, unbiased and cost-effective DNA based assay. Therefore, in present study the polymorphic survey of several microsatellite markers was conducted to identifying SSR markers that can distinguish parental lines of rice hybrids and access their genetics purity.