Recently published phylogenetic analyses of 52 strains of Navicula cryptocephala-like diatoms confirmed the existence of genetically distinct lineages within N. cryptocephala: clade I "RBG" and clade II "Lubnaig". Using geometric morphometry, we compared strains of both clades with the lectotype and found that clade I represents N. cryptocephala sensu stricto, while clade II constitutes a different taxon, for which we establish a new species, Navicula lothargeitleri sp. nov.
Both species can be distinguished by their interphase nucleus structure. Slight differences in valve morphology are described and discussed.