Because of the rapid fluctuation in world's climate, politics, and economy, maize outputs must be increased to meet food security demands. Due to the importance of the genetic materials under study as a source of quality traits and genetic variability, this study was designed to examine the effectiveness and strength of assessing biodiversity in some maize hybrids using barcodes and molecular SCoTs markers in addition to phytochemical characterization. Using matK and rbcL sequences, pairwise distances were obtained and assessed. The hybrids under study were distributed into different groups based on the matK and rbcL sequences. The 12 SCoT primers amplified 155 amplicons with an average of 12.92 bands per primer, of which 63 monomorphic bands (MB) (40.65 %) and 92 polymorphic band (PB) (59.35 %). Additionally, the number of unique bands was six bands. The SCoT-6 primer produced three bands individually, while the primers SCoT-2, SCoT-3, SCoT-4, and SCoT-7 produced one band each. Hybrids S.C. 10, S.C. 128, S.C. 130, S.C. 131, S.C. 132 and TWC. 324 were more influenced by some primary constituents and bioactive secondary compounds such as moisture content (%), crude fiber, total carbohydrates, total sugars, soluble carbohydrates, non-reducing sugars, phenolics compounds, and tannins. The hybrids S.C. 168, S.C. 176, S.C. 178, TWC. 360, TWC. 368 and TWC. 321 were more influenced by the SCoT molecular markers. The results of genetic variation between the studied hybrids could be considered a potentially source of genetic information in developing future breeding programs.