The focus of this paper is the sexual reproduction and phylogeny of Schizostauron Grunow, which were studied using clonal cultures isolated from the Indian Ocean coast of Mozambique near Tofo and Bazaruto. Taxa of Schizostauron were characterized by light and electron microscopy and a phylogeny derived from three genes (rbcL, psbC and short subunit). Schizostauron was established in the second half of the 19th century, then forgotten, with its taxa included in Cocconeis or Achnanthes sensu lato. Schizostauron, together with Astartiella and perhaps also Kolbesia and Karayevia, seems to form a third lineage of monoraphid diatoms, which are related to biraphid diatoms belonging to the Stauroneidaceae and Parlibellus, but not to the two other lineages of monoraphids (Achnanthes and the Achnanthidiaceae–Cocconeidaceae group). In culture, size reduction was followed by release of gametes and auxosporulation in mixtures of clones. Despite some morphological differences, four clones from the Bazaruto population proved to be sexually compatible, one of the clones being sexually compatible with the three others. Before gametogenesis, cells gathered in groups of two to eight through active movement. Some groups of cells surrounded themselves by weakly visible mucilage. Reproduction was isogamous morphologically, and apparently also behaviourally. Growing auxospores were surrounded by the empty irregularly arranged frustules of parental cells. In numerous aspects the pattern of sexual reproduction of Schizostauron is similar to that of Achnanthes sensu stricto. The rbcL identity matrix (IDM) for sexually compatible clones ranged between 0.998 and 0.984. One clone derived from the Tofo population had an IDM below 0.900 and was sexually isolated from the remaining clones. A description of Schizostauron davidovichiorum sp. nov. is provided.