Investigations on the littoral microphytobenthos populations of lakes are very rare. Based on new sampling techniques, allowing the undisturbed sampling of sublittoral sediments, we present information on limnic microphytobenthos populations of the Schöhsee in Northern Germany (10° 26'E, 54° 13'N). Investigations on microphytobenthic communities at a sandy and a muddy site provided new insights into the community structure and seasonal variations of limnic benthic microalgae. The microphytobenthos was characterised by low chlorophyll-a contents (0.16 μg cm -2 to 0.74 μg cm -2) and low cell numbers (25 cells cm -2 to 266 cells cm -2). Both sites showed similar patterns in terms of algal biomass and seasonality; no site-specific characteristics were observed. The productivity of the sediment microflora in the Schöhsee was low and most likely related to the mesotrophic lake character and to reduced light conditions in the near-shore sublittoral. The algal communities at both sites showed high diversity, distinct seasonality and succession patterns with shifts in community composition in spring, summer and autumn. The community was dominated by Fragilaria spp., Navicula spp., Nitzschia spp., and Stauroneis spp. in spring shifting to a Stauroneis spp.-dominated community in summer. In autumn the populations were dominated by Navicula spp., Nitzschia spp., and Stauroneis spp. Overall, the taxonomic composition showed a dominance of prostrate diatoms, whereas cyanobacteria, green algae and erect diatoms occurred rarely and with low abundance. Thus, the sediment microflora of the Schöhsee can be characterized as a flat, two-dimensional community. © 2006 E. Schweizerbart'sche Verlagsbuchhandlung.