This article reviews current knowledge of wall morphogenesis in pennate diatoms in relation to the way characters are defined and described for taxonomic and systematic analyses. It argues that an understanding of ontogeny is essential for the accurate identification of character homologies, which in turn must underpin all phylogenetic and systematic analyses. Terminology should reflect character homology, but most diatom terminology fails to do this, with concomitant confusion and potential taxonomic mistakes. Identifying where information is lacking or misinterpreted are first steps toward improving our understanding of diatom structure and relationships. After reviewing the current knowledge on pennate diatom structure and its development, this article briefly discusses the significance of morphological variation, character polarity, and the vital importance of applying diatom terminology correctly.