Ninety-eight genotypes (40 genotypes of Balam, 27 of Jesso-Balam, 21 of Kartiksail and 10 of Dhaliboro groups, respectively) of similar or duplicate named rice accessions along with HYV’s were studied for quantitative, qualitative and molecular characters at Bangladesh Rice Research Institute during 2009-12. For estimating diversity level, the genotypes were divided into five populations. The PIC ranged from 0.50 (Dhaliboro) to 0.74 (Balam) with 0.69 for HYVs, indicating the existence of more diversity and broader genetic base in Balam land race cultivars. Similarly, genetic diversity with an average of 0.83 ranged from 0.55 (Dhaliboro) to 0.77 (Balam) and 0.73 for HYV’s. The Shannon’s information index ranged from 1.00 (Dhaliboro) to 1.73 (Balam) and it was 1.48 for HYV’s. The number of different allele ranged from 3.56 (Dhaliboro) to 7.80 (Balam), while the number of effective allele from 2.63 (Dhaliboro) to 5.11 (Balam) and it was 5.18 and 4.14 for HYV population, respectively. Analysis of molecular variance showed that the maximum percentage of variation was present among individuals within populations (85%), followed by among populations (15%). The spearman’s rank correlation coefficient was found highly significant (rs=0.51; t=2.98) between ranking of inter-genotype (D=√D2) and Nei’s genetic distances, indicating strong association between them. The correlation tests revealed that SSR diversity analysis is the most powerful method for grouping. But, combination of quantitative and molecular methods may be the best. Finally, 21 core collections were selected from Balam group. The selected core accessions need to conserve as active collection in Genebank, utilize as parents in hybridization programs and develop QTL map for unlocking valuable genes.