Microsatellite markers were used for fingerprinting of hybrids, assessing variation within parental lines and testing the genetic purity of hybrid seed lot in rice. In this study, 10 simple sequence repeats (SSR) markers were employed for fingerprinting 2 popular rice hybrids of north India along with one pipe line hybrid (PSD1,PSD3 and UPRH101) and their parental lines i.e. two CMS lines (UPRI 95-17A and UPRH101A) and two restore lines (UPRI 92-133 and UPRI 93-287. Among the 10 primers studied: RM1, RM154, RM164, RM171, RM204, RM206, RM216, RM337, RM263, RM1108 and RM6345, and all showed polymorphism between the parental lines which were used for the identification of rice hybrids PSD1, PSD3 and UPRH101. A set of four markers (RM1, RM 154, RM337 and RM 1108 among the 10 markers) differentiated all the hybrids from each other, which can be used as referral markers for unambiguous identification and protection of these hybrids. The study of DNA profile revealed that the CMS as well as restore line showed only one band and hybrid showed two bands of respective parents. The SSR markers identified both bands of female and male in their respective parents useful in genetic purity testing of hybrid.