Abstract: Clitoria ternatea L.(Family: Fabaceae) comprises two varieties, namely, C. ternatea var. ternatea (Papilionaceous form) and C. ternatea var. pleniflora (Non-papilionaceous form).The proposed study compared seven morphotypes of C. ternatea exhibiting different flower colors and symmetry with their profiled bioactive metabolites and ISSR markers.A phytochem. study was performed on fresh floral methanolic extracts to estimate total flavonoid, total anthocyanin (Cyanidin and Delphinidin equivalent), and total phenolic content.The genotypes showed varied amounts of these constituents, with the highest quantities found in the Single Blue morphotype for phenolic and Cyanidin equivalent, while the Double Blue morphotype exhibited the highest flavonoid and Delphinidin content.The antioxidant potential of the Double Blue morphotype was comparable to ascorbic acid in the DPPH radical scavenging assay.Addnl., ISSR markers effectively distinguished morphotypes based on floral color and symmetry.From an initial 30 primers, 20 generated clear, reproducible polymorphic bands.UBC 868 amplified the highest number of bands, while UBC 890 showed complete monomorphism across all varieties with 21 monomorphic bands.The average resolving power was 2.267, and UBC 810 demonstrated significant discriminating power among morphotypes.UBC 855 revealed distinctive patterns in double petal forms, whereas UBC 872 served as a floral color-specific marker, differentiating blue morphotypes from others.This study helps to compare the intraspecific variants differing in color and floral architecture, establishing a correlation between phytochem. profiles and petal coloration, thereby enhancing the understanding of this species′ diversity.