Characterization of genetic diversity is the foundation step for crop improvement, which provides a basis for analyzing combining ability and heterosis of inbred genotypes during a hybridization program. An investigation was carried out at the field laboratory of the Genetics and Plant Breeding department in Bangabandhu Sheikh Mujibur Rahman Agricultural University, to elucidate the genetic architecture by evaluating 12 morphological and 4 molecular (SSR) markers within 52 diverse S1 genotypes, and to assess the relationship of molecular and morphological GD. An almost equal amount of PCV and GCV coupled with high heritability and genetic advance for the traits cob weight (gm), NKPC, and NKPR lead to the selection of promising genotypes based on these characters. Correlation coefficient and scatter plot matrix established a positive and strong relationship of KL (mm), KW (mm), and KT (mm) with 100 kernel weight (gm) suggesting the importance of kernel morphology. Mahalanobis D2 statistics revealed the highest inter-cluster distance between I and II. The percentages of molecular variance within the population and among the population were 76% and 14 %, respectively. The optimum K-value was 5. Heatmap relying on molecular GD exposed MMIL-28, MMIL-54, and MMIL-96 as the most diverse lines. SHE analysis hypothesized the increase of richness and diversity over time. Less correlation between the divergence generated from morphological traits and molecular markers suggested that the morphological variation may be determined by environmental factors and also by genetic factors. A strategy for the effective selection of predicting parental lines for a future hybridization program was developed.