Morphological and molecular markers were used for fingerprinting of hybrids, assessing variation within parental lines and testing of genetic purity of hybrid seed lot in rice. Conventionally, genetic purity of hybrids is assessed by grow out test (GOT). The distinguishing characters were used for the identification of hybrids from the lot, but it takes one full season. In order to reduce this time, molecular markers can be used as tools. In the present investigation, sixteen SSR markers were employed for finger printing of 3 rice hybrids and their parental lines. Eight primers amplified a maximum of two alleles whereas, all other were detected as monomorphic. Genetic purity of hybrid JRH 5, the SSR markers RM 234, RM 228, RM 84, RM 279 and RM 237 were identified. However, to test the genetic purity for JRH 8 and JRH 19, markers RM 234, RM 228, RM 279 and RM 510 were identified for testing the purity of these hybrids. Thus from this study it might be concluded that the molecular markers greatly augmented the entire process of testing genetic purity of hybrid seeds, by saving one full crop season and reducing the cost of hybrid seed.