A small marine monoraphid diatom with a linear-elliptic shape and simple terminal raphe endings was present on Raivavae (South Pacific). Particularly due to its different stria structure on both valves, this taxon is here classified as Cocconeis. The new species was present on the rocky intertidal shore of the coral-reef lagoon, as an epiphyte on a turf. Cocconeis vaiamanuensis sp. nov. can be compared to some other monoraphids with a simple raphe system and a rod-like shape. The new taxon has small marginal processes on the sternum valve (SV) mantle, as previously reported for Cocconeis peltoides. Such processes were also previously observed in Platessa and Psammothidium. A cladistic analysis based on ultrastructure shows an affiliation between several close-by taxa. Cocconeis of the C. peltoides section are close to Psammothidium, whereas other Cocconeis without processes are closer to Platessa and Achnanthidium. A clone of Cocconeis cf. sigillata (SZCZCH1200) allowed for a molecular phylogeny to be reconstructed. The molecular signature of Cocconeis cf. sigillata is close to that of Lemnicola hungarica. Cocconeis is a genus with different and complex morphologies that may be split into independent clades (genera). The SV processes may be a vestigial character reminiscent of an ancestral state.