Sixteen monoclonal strains classified into six morphotypes typical of, or close to, intraspecific taxa of Pseudopediastum boryanum, including P. alternans (ALT), P. boryanum var. boryanum (BOR), P. boryanum var. cornutum (COR), P. boryanum var. forcipatum (FOR), P. boryanum var. longicorne (LON), and P. boryanum var. perforatum (PER), were simultaneously subjected to phylogenetic (26S rDNA and rbcL cpDNA) and morphometric analyses. Marginal cell shape, coenobium and cell size, and granule density on the cell surface were analyzed statistically. The shapes of some morphotypes (BOR, COR, FOR, and PER) were also compared to the shapes of corresponding type illustrations. Pseudopediastrum boryanum var. boryanum, without any reliable morphological and phylogenetic data, appeared to be a questionable taxon that needs a neotype. The variety longicorne proved to be a complex taxon that should be split after morphometric data of more strains and of the corresponding lectotype are included in the statistical analysis. A new species, Pseudopediastrum oblongum, was described, and four varieties were elevated to the species level, which resulted in establishing new combinations, P. cornutum, P. forcipatum, P. perforatum, and P. subgranulatum. Reference sequences for the new species and combinations were obtained. The paleoecological value of P. boryanum sensu lato appeared to be limited by the relatively low percentage of marginal cells typical of particular varieties and a high risk of their misidentification in the light microscope. The shape of marginal cells seemed to be the best diagnostic feature. Granule density could be helpful to discriminate between certain taxa.