Autotrophic picoplankton (APP) abundance, primary production and vertical distribution were studied in the oligotrophic Lake Stechlin (northeastern Germany) in 1994 and 1995. Within the euphotic zone APP contributed 34% of phytoplankton biomass and 35% of primary production. Annual average APP cell number was 209×103 cells ml−1, of which 95% were unicellular cyanobacteria, 2% were colonial cyanobacteria and 3% were eukaryotes. Three ecologically and/or morphologically different groups of APP were recognized: (i) unicellular cyanobacteria belonging to the genus Cyanobium, (ii) eukaryotic species growing in early spring under isothermal conditions and (iii) cyanobacteria, partly colonial species, growing in the stratified period in the euphotic zone. Three species of eukaryotic green algae were identified: Choricystis minor, Neocystis diplococca and Pseudodictyosphaerium jurisii, the latter two being colonial. This is the first record of the occurrence of colonial eukaryotes potentially of APP size in fresh waters. In summer picocyanobacteria were highly productive so the low net increase rates indicate that losses must be high. The dominant, Cyanobium population started growing in February with maximum abundance in late April, contributing significantly to the spring peak in phytoplankton biomass. During this growth period, the population was evenly distributed in the 60 m water column. By the time the maximum biomass occurred, inorganic nutrients had decreased below analytically detectable levels. Parallel to the onset of stratification a part of the population was grazed, most probably in the microbial loop and primarily in the upper 10–15 m. The rest of the Cyanobium population accumulated in a narrow layer in the upper hypoliminon. The APP remaining from the spring was persistent for much of the summer in this cold, high-nutrient (especially nitrate)/low-light environment. Short phosphorus-turnover times suggest that APP is probably phosphate-limited. The stability of the thermocline and the pattern of thermocline development in May affected the accumulation of the APP cells in the upper hypolimnion. Thus, this process is sensitive to the physical stability of the water column.