Conventional and landmark-based geometric morphometric approaches were used to clarify the taxonomic identity of a centric diatom morph. This morph, found in cultures isolated from the Geeste estuary (Northern Germany), showed an intermediate valve morphology between that of typical specimens of Cyclotella meneghiniana Kützing and of C. scaldensis Muylaert & Sabbe. Its internal valve ultrastructure was compared to that of cells from 1) cultures of C. meneghiniana isolated from the same field samples and grown in the same conditions, 2) field material from the samples from which the cultures were isolated, and 3) a sample from the type locality of C. scaldensis. The morphometric analyses were used to determine 1) whether morphological variation of these morphs was continuous, or whether there were distinct morphological groups, and 2) how effective the alternative morphometric approaches were in answering this question. Both approaches proved informative and their results complemented each other, supporting the conclusion that three distinct size-reduction series were present in the samples investigated. Since the different morphs occurred sympatrically, we suggest that they probably belong to three reproductively isolated species.