Background – The traditional approach to diatom systematics assumed that structure and morphology were stable within a taxon and replicated faithfully down the generations, but wall structure is the end-product of biological processes, potentially modified by environment and over time. Electron microscopy revealed additional structural characters that may be taxonomically informative, but homology continues to be inferred primarily on morphological similarity, without reference to ontogeny. Review – Morphogenetic data reveal that similar structures can be derived in different ways, and that dissimilar end-products may be produced by a single ontogenetic pathway. This paper discusses the importance of understanding valve morphogenesis before wall characters and character states are chosen and described, with particular reference to dorsiventrality, solid areas of silica, raphe and pore structure. Conclusions – A better understanding of character formation will inform the use and development of terminology, which is critical to comparative studies and phylogenetic analyses of morphological data.