Seeds of the local rice varieties were collected from Genetic Resource and Seed Division (GRSD) of Bangladesh Rice Research Institute (BRRI). The varieties were grown and molecular characterizations were done in the Genetic Fingerprinting Laboratory of the Department of Genetics and Plant Breeding during the period of August/2008- January/2009. 10-12 seeds of each variety were selected randomly and dried in oven at 540C for 48 hrs for better germination. After germination in the wet blotting paper in petridishes, the seedlings were grown in small plastic pots. Bulked DNA was isolated from 2-5 juvenile culms of 15-day-old seedlings of each of 28 rice varieties/cultivars following the protocol described by Aljanabi and Martinez (1997) and also used by Rahman et al., (2007) with some modifications. Excluding usage of CTAB, the modified protocol included digestion with homogenization buffer (Solution: Tris-50 mM, EDTA-25 mM, NaCI-300 mM, 1% SDS and deionized water) at 650C for 30 min, extraction with phenol: chloroform: isoamyl alcohol (25:24:1), precipitation with ice-cold and extra pure isopropyl alcohol and purification with absolute ethanol (Plus sodium acetate, 3M) and 70% ethanol chronologically. Finally, DNA sample of each rice variety dissolving in 30-40μl of TE buffer within 1.5 ml eppendorf tube was preserved separately at -20°C. Presence of genomic DNA was confirmed on 1% agarose gel qualitatively. The amount of genomic DNA was quantified at 260nm spectrophotometrically (Spectronic® GenesisTM). Using the absorbance reading obtained for DNA sample of each rice variety, the original DNA concentrations were determined and adjusted to 25 ng/μl. A set of seventeen microsatellite primer pairs (RM5, RM55, RM105, RM151, RM153, RM170, RM206, RM264, RM266, RM278, RM287, RM307, RM333, RM334, RM335 RM475 and RM481) distributed in the rice genome were identified from the available data-based search (http://www.gramene.org/) for rice SSR markers as described by Akagi et al. (1996), Panaud et al. (1996), Temnykh et al. (2000, 2001) and McCouch et al. (2002). From those identified primers, at first 3 to 5 primers were tested against 5 randomly selected varieties with a recommended PCR thermal profile. Based on better responsiveness in amplifying the target genomic region of template DNA, the expected PCR product sizes in base pairs was then going to check. The selected Primers were then screened against 28 varieties at a time. In this way seven primer pairs viz. RM153, RM206, RM251, RM307, RM333, RM335 and RM475 representing chromosome numbers 5, 11, 3, 4,10, 4, and 2 of rice genome (Temnykh et al., 2001) with clear and expected amplified product sizes were selected and used for microsatellite analysis in the present study. One (RM153) and two (RM153 and RM335) of these primers were used in the study for molecular characterization of 34 rice varieties (Rahman, et al., 2006) and 94 rice varieties (Rahman, et al., 2007) respectively. Polymerase chain reaction (PCR), Electrophoretic separation and visualization of PCR products and Scoring and analysis of microsatellite data were recorded.