Morphological, anatomical, and molecular information facilitates the identification and inference of the relatedness of plant species. In this study, the macromorphological, micromorphological, and anatomical characteristics of nine species from the Brachychiton and Sterculia genera belonging to the Malvaceae family were examined by light and a scanning electron microscope. The study recorded 66 macromorphological, micromorphological, and anatomical characteristics, thus revealing important variations between the studied species in leaf morphology and anatomy. This included variations in leaf complexity, leaf arrangement (phyllotaxy), epidermal cell walls, and their sculpture, as well as in the types of glandular and non-glandular trichomes. The studied species were mostly conserved in shedding patterns, being evergreen only in one out of nine studied species. Similarly, eight species were petiolate. Conversely, leaf arrangement and leaf complexity characteristics were highly divergent among the studied species, though only one species, Sterculia foetida, had compound leaves. The differences in the studied features and the chloroplast genes MaturaseK (MatK) and ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcl) were exploited to deduce the relationship between the studied species. While the morphological and anatomical features demonstrated a close relationship between the studied intrageneric species, the DNA barcoding analysis proved very efficient in distinguishing the two neighboring genera. Collectively, the different clustering analyses suggest a close relatedness between Brachychiton acerifolius and B. australis, while only DNA-based clustering demonstrates cladistic monophyly of the Sterculia species. This study, therefore, provides a detailed description of various morphological and anatomical features important for the systematic studies within the Malvaceae family and highlights the value of incorporating morphological, anatomical, and molecular approaches for inferring the evolutionary relationship between closely related plant species.