The fine structure and ontogeny of sexual stages from cultures of the domoic-acid-producing dioecious pennate diatom Pseudo-nitzschia multiseries were examined by scanning electron microscopy. The structure of gametangia, position of the gametes relative to the gametangia, and their sequential maturation observed previously using light microscopy were confirmed in our material. As well, the general structure of the auxospore conforms to the pattern of development in many previously investigated pennate diatoms. Scales were observed in the gamete wall as well as in the internal lining of the primary wall of the auxospore. Scales in gamete walls were not found previously in any diatom, while in the primary auxospore wall they were known only in three other species. The presence of scales in sexual stages of the morphologically advanced diatom P. multiseries supports the monophyletic origin of diatoms and their relationship to the scale-bearing ancestors. The initial cell divides once while still within the auxospore. It may thus exit by piercing the apex of the perizonium when one of the sibling cells slides along the other during the first vegetative division. Initial epivalves show several morphological irregularities compared to typical vegetative valves; the initial hypovalve may bear a more typical morphology. Finally, we discovered a correlation between the molecular (ssu tRNA) phylogeny of diatoms and the basic types of auxospores. The lack of similar reports from other species may be attributed to the scarcity of investigations into the fine structure of sexual cells in diatoms. Similarly, scales may be found more commonly when other species are carefully examined. Then, gamete and auxospore structure may prove useful in defining higher rank taxa in the natural phylogeny of diatoms.