The pattern centre in valve morphogenesis is an annulus in centric diatoms or a sternum in pennate diatoms. The genus Rhaphoneis is currently placed within a lineage that diverges at the root of the pennate diatom clade in most molecular phylogenies, and its valves have a unique pattern to their striae, i.e. radiating from both apices, giving the impression that a pattern centre exists at both ends of the valve and virgae (ribs) formation proceeds centripetally. The present study, however, shows that the pattern centre is actually a linear sternum and the formation of virgae proceeds centrifugally, a pattern centre that is commonly found in most araphid diatoms. Thus, the hypothesis that valve morphogenesis based on a linear sternum and perpendicular virgae is a synapomorphy of pennate diatoms is supported. Our study also demonstrates that the pattern of valve formation can be observed by light microscopy with a direct mounting method when the specimen is relatively large, i.e. exceeding approximately 50 µm in valve length. An important advantage of the use of the direct mounting method is that it requires no repeated centrifugation steps for dehydration, steps necessary for observation by a scanning electron microscope, causing the loss and/or collapse of the specimen, particularly with fragile valves in the early stages of development.