Plant morphology, including morphogenesis, remains relevant to practically all disciplines of plant biology such as molecular genetics, physiology, ecology, evolutionary biology and systematics. This relevance derives from the fact that other disciplines refer to or imply morphological concepts, conceptual frameworks of morphology, and morphological theories. Most commonly, morphology is equated with classical morphology and its conceptual framework. According to this, flowering plants and certain other taxa are reduced to the mutually exclusive categories of root, stem (caulome) and leaf (phyllome). This ignores the fact that plant morphology has undergone fundamental conceptual, theoretical and philosophical innovation in recent times. These changes, when recognized, can fundamentally affect research in various disciplines of plant biology. They may even change the questions that are asked and thus may affect the direction of future research. If, for example, plant diversity and evolution are seen as a dynamic continuum, then compound leaves can be seen as intermediate between simple leaves and whole shoots. Recent results in molecular genetics support this view. Phylogenetically, this could mean that compound leaves are the result of developmental hybridization, i.e. partial homeosis. Many other examples are given to illustrate the relevance and potential impact of basic conceptual and theoretical innovations in plant morphology.