Ninety six T. Aman, 48 Aus and 20 Geographical Indication (GI) rice landraces were used as test materials for molecular characterization and genetic diversity study using 12 (RM60, RM163, RM218, RM237, RM259, RM125, RM278, RM283), 14 (RM6, RM204, RM241, RM279, RM519, RM286, RM44, RM147, RM107, RM118, RM10, RM161, RM1, RM85) and 12 SSR markers (RM5, RM85, RM163, RM180, RM189 RM266, RM271, RM286, RM314, RM408, RM470, RM519), respectively at GRS Division of BRRI during 2012-13. DNA was extracted from young leaves of 3-week-old plants following a simple and modified protocol as described by Zheng et al. (1995) for PCR analysis. PCR was performed in 12.5 µl reaction containing 5-25 ng of DNA template, 1.25 µl of MgCl2 free 10X PCR buffer (100 mM Tris-HCl pH 9.0 at 25°C, 500 mM KCl, 0.1% Triton® X-100 and H2O), 1.5 µl of 25 mM MgCl2, 0.25 µl of 10mM dNTP, 0.25 µl of 5 U/µl Taq polymerase enzyme, 0.625 µl each of 10 µM forward and reverse primers using a MJ Research single 96 well thermal cycler. The mixture was overlaid with one drop of mineral oil to prevent evaporation. After initial denaturation for 5 minutes at 94°C, each cycle comprised 1 min denaturation at 94°C, 1 min annealing at 55°C, and 2 min extension at 72°C with a final extension for 7 min at 72°C at the end of 35 cycles. The PCR products were mixed with bromophenol blue gel loading dye and were analyzed by electrophoresis on 8% polyacrylamide gel using mini vertical polyacrylamide gels for high throughput manual genotyping (CBS Scientific Co. Inc., CA, USA). The 2.5 µl of amplification products were resolved by running gel in 1xTBE buffer for 2-2.5 hrs depending upon the allele size at around 75 volts and 180 mA current. The gels were stained in 0.5 mg/ml ethidium bromide and were documented using UVPRO (Uvipro Platinum, EU) gel documentation unit. All data were analyzed in computer using Alpha-Ease 5.0 software, Power Marker version 3.25 (Liu and Muse, 2005) and NTSYS-pc version 2.2 (Rohlf, 2002).