Hibiscus is a charismatic genus of the Malvaceae family that is noted for its diversity, lacking identifiable characteristics for distinguishing its various species. Therefore, there is an urgent need to develop authentication methods for genus delimitation and species delineation. The present study aims to discern the taxonomic relationships between the well-known, globally familiar, and economically important five Hibiscus species, namely: H. × rosa-sinensis, H. sabdariffa, H. schizopetalus, H. syriacus and H. tiliaceus based on traditional morphological and anatomical characteristics compared to the contemporary chemotaxonomy. In this context, the leaf-based methanolic extracts of the studied species were analyzed by Gas Chromatography-Mass Spectrometer (GC–MS) to estimate their secondary metabolites similarity. In addition, selected qualitative morphological and anatomical traits including leaf venation patterns, epidermal micromorphology, stomata types and trichomes diversity, petiole serial sectioning (outline, adaxial groove features, vasculature traces arrangement), and midrib characteristics of the studied species were investigated. The results of both chemotaxonomy and traditional taxonomy exhibited a remarkable agreement in the delineation of the five studied species. Specifically, the chemotaxonomy-based dendrogram separates the studied species into two main clusters with the H. sabdariffa as an outlier species in a single cluster and the remaining four species as another cluster with variant distances in its similarity indices. Similarly, the traditional morphological and anatomical characteristics revealed distinct traits for H. sabdariffa compared to the remaining four species. The findings of this study highlight the significance of integrating the structural features with phytochemicals profiling as a potential approach that could be harnessed for the delineation of the taxonomically challenging Hibiscus genus.