Although the number of morphological characters provided by diatom frustules for species identification is unparalleledamong unicellular eukaryotes, morphology alone has in several cases proven to be insufficient to detect species boundaries inthis algal group. Our recent nuclear rDNA sequence survey indicated that Cyclotella meneghiniana, one of the most intensivelystudied freshwater diatoms, is another example of a species complex. We therefore sampled genetic variation in the D1/D2regions of the nuclear 28S rDNA and in a segment of the plastid encoded psaA gene in a larger sample of C. meneghiniana15 strains to assess genetic diversity and genetic structure over a wider geographic range within this diatom. A strict congruenceof nuclear rDNA and psaA variants was observed, indicative of the presence of eight genetically distinct, cryptic lineages, fourof which were not represented in our previous study. To test whether the genetic structure is caused by the complete lack ofallogamy, or by the presence of reproductive barriers between allogamous cryptic species, we generated AFLP fingerprintsfrom two subsamples of sympatric strains. Phylogenetic incompatibility in AFLP banding patterns did not differ significantly20 from panmictic expectations. Therefore, we suggest that C. meneghiniana is a complex of several, reproductively isolated,sexual species, rather than a complex of either strictly self-fertilizing or clonal lineages.