Water stress, one of the devastating abiotic stresses in rainfed rice ecosystems causes huge loss to rice yields. Enhancement of production as well as productivity in rainfed areas requires development of improved varieties for such regions. Slow progress in drought breeding is an impediment in this way. Marker assisted approach is an alternative for fast track improvement of crops for drought. Validation of QTLs associated with drought related traits across the populations would add value to their application. In the present study, two SSR markers RM60 and RM252 reported earlier for root thickness were evaluated for their association with a set of DH lines derived from the cross of CT9993 IR68766 and recombinant inbred lines (RILs) derived from cross of IR66366 IR66876 as well as on a set of twenty cultivars / landraces of rice adapted to the rain fed lowland and upland ecosystems. The marker RM252 was consistently associated with the root thickness in all these cultivars and populations, and is therefore suitable for adoption in marker assisted selection for the root thickness and penetrating ability. The other marker, RM60 distinguished the thickrooted and thin-rooted parents, CT9993 and IR68566, showing higher and lower molecular weight alleles, respectively, but it did not show one to one association with the thick and thin rooted phenotypes among the RILs. Besides, RM60 could not be validated in the RILs of IR66366 and IR66876 because it did not show polymorphism. The association of RM252 was much stronger than that of RM60. Marker assisted improvement through this approach can be applied for QTL transfer in multiple genetic backgrounds.