1. We used flow cytometry to characterize freshwater photosynthetic picoplankton (PPP) and heterotrophic bacteria (HB) in Lake Kivu, one of the East-African great lakes. Throughout three cruises run in different seasons, covering the four major basins, phycoerythrin-rich cells dominated the PPP. Heterotrophic bacteria and PPP cell numbers were always high and spatial variations were modest. This represents an important difference from temperate and high latitude lakes that show high fluctuations in cell abundance over an annual cycle. 2. Three populations of picocyanobacteria were identified: one corresponded to single-cells (identified as Synechococcus by epifluorescence microscopy, molecular methods and pigment content), and the two other that most probably correspond to two and four celled colonies of the same taxon. The proportion of these two subpopulations was greater under stratified conditions, with stronger nutrient limitation. 3. High PPP concentrations (c. 10 cell mL) relative to HB (c. 10 cell mL) were always found. Lake Kivu supports relatively less bacteria than phytoplankton biomass than temperate systems, probably as a consequence of factors such as temperature, oligotrophy, nutrient limitation and trophic structure. 4. A review of PPP concentration across aquatic systems suggests that the abundance of Synechococcus-like cyanobacteria in large, oligotrophic, tropical lakes is very high. 5. Photosynthetic picoplankton cell abundances in the oligotrophic tropical lakes Kivu and Tanganyika are comparable to those of eutrophic temperate lakes. This apparently contradicts the view that PPP abundance increases with increasing eutrophy. More data on PPP in tropical lakes are needed to explore further this particular pattern.