The verification of taxonomic identities is of the highest significance in the field of biological study and categorization. Morpho-molecular characterization can clarify uncertainties in distinguishing between taxonomic groups. In this study, we characterized five local taxa of the genus Cichorium using morphological and molecular markers for taxonomic authentication and probably future genetic improvement. The five Cichorium taxa grown under the Mediterranean climate using morphological traits and molecular markers showed variations. The examined taxa showed a widespread range of variations in leaf characteristics, i.e., shape, type, texture, margin, and apex and cypsela characteristics i.e., shape, color, and surface pattern. The phylogenetic tree categorized the Cichorium intybus var. intybus and C. intybus var. foliosum in a single group, whereas C. endivia var. endivia was grouped separately. However, C. endivia var. crispum and C. endivia subsp. pumilum were classified as a cluster. The recorded variance between classes using the molecular markers SCoT, ISSR, and RAPD was documented at 34.43%, 36.62%, and 40.34%, respectively. Authentication using molecular tools proved the usefulness of a dichotomous indented key, as revealed by morphological identification. The integrated methodology using morphological and molecular assessment could support improved verification and authentication of the various taxa of chicory. It seems likely that the Egyptian chicory belongs to C. endivia subsp. pumilum.