Cocconeis nosybetiana sp. nov. is described from Nosy Be Island (Madagascar, Indian Ocean). This taxon is characterized by its sternum valve (SV) with ‘diabolo-like’ areolae (hymenes/ supported by two transapical pegs), by its round valve shape and its raphe valve valvocopula (RVVC) with irregular short fimbriae and simple papillae. The raphe valve (RV) of the new taxon shares many similarities with that of Cocconeis scutellum Ehrenberg, except for its RVVC. Com- parison of the new species with allied taxa, particularly C. scutellum var. posidoniae f. decussata, is provided. In this case, the two taxa mainly differ in the structure of the SV areolae, which have an apical complete bar in place of transapical short pegs in C. nosybetiana. Furthermore, the shape of the valve, the RV stria density, as well as the fimbriae and papillae of the RVVC are different between the two latter taxa. The role of recent EM technologies on the morphological discrimina- tion of close taxa is discussed.