In this paper, the morpho-agronomic diversity of rice in F2 generation were further analyzed. A total of 20 genotypes (Sintanur and Logawa as parents, 9 genotypes F2 SL (Sintanur x Logawa), 9 genotypes F2 LS (Logawa x Sintanur)) were investigated for culm color, plant height, flowering time and harvest time. Data were binary-coded for each genotype and calculated using Jaccard’s coefficients, and then were used to construct dendrogram using UPGMA employing the SAHN from the MVSP 3.1. software. Heritability and inbreeding depression were analysed. Analysis of morpho-agronomic diversity showed there were two groups in the coefficient of 0.15. The dendrogram obtained contained two main groups, with SL-2-6 genotype is an effective out-group. The origin of the genotypes was not always related to the cluster. The highest heritability was found for plant height. Negative inbreeding depression was revealed by majority of the F2 population. Construction of diversity can be done using morpho-agronomic and the use of these will allow a quick selection. The result result indicated that F2 generation showed diversity and the strong potential usage for further advanced in low glycaemic index and fine grain rice breeding.