Identifying the best performing hybrid without a field test was essential to save resources and time. In this study, the genetic divergence was estimated using morphological and expressed sequence tag (EST)-derived simple sequence repeats (SSR) markers. Cluster analysis showed that APMS6A and RPHR 1005 belong to groups I and II, respectively, and the hybrid combination recorded the highest mean grain yield of 32.25 g among generated 40 F1s with standard heterosis of 8.4% over hybrid check, KRH2. The coefficient of marker polymorphism (CMP) value was calculated based on EST-SSRmarkers; it ranged from 0.40 to 0.80, and a higher CMP value of 0.80 was obtained for the parental combination APMS6A × RPHR1005. We predicted heterosis for 40 F1s based on correlation between CMP and standard heterosis in different traits with standard varietal and hybrid checks indicating positive correlation and significant value for grain yield per plant (r = 0.58**),productivity per day (r = 0.54**), productive tillers (r = 0.34*) and panicle weight (r = 0.42**). This study revealed that the relationship of molecular marker heterozygosity, along with the combining ability, high mean value of different traits,grouping of parental lines based on morphological and molecular characterization is helpful to identify heterotic patterns in rice.