Photosynthetic picoplankton (PPP), particularly picocyanobacteria (PCya), are known to be a major component of phytoplankton in oligotrophic waters. We investigated the dynamics of PPP and heterotrophic bacteria (HBact) in Lake Tanganyika during the dry and rainy seasons of 2004 to 2007, in the two basins of this large lake. Flow cytometry analyses showed that PPP was mainly composed by PCya of the phycoerythrin-rich Synechococcus type, with maximal abundances (2.3 × 10-8.2 × 10 cells mL) found in the mixolimnion (10-20 m depth). PPP biomass integrated over the water column depth ranged between 0.41 and 3.09 g C m, with maximal values in the south basin during the dry season (2.28 ± 0.62 g C m on average). The contribution of PPP to total phytoplankton biomass ranged from 41 to 99, with highest values in the south basin in the dry season. Cellular measurements by image analysis of epifluorescence microscopy images showed a significant increase of the cell volume of the PCya during this period. Flow cytometry also allowed enumeration of photosynthetic picoeukaryotes. Assuming a conversion factor of 530 fg C cell, they contributed on average to 6 to PPP biomass, except during the dry season in the south basin, where their contribution increased to up to 20 of PPP biomass. Integrated over a 100-m water column depth, PCya biomass was on average 1.4 times higher than HBact biomass. This study establishes reference values for the biomass contribution of this part of the microbial food web, covering for the first time, spatial (different sites), vertical (profiles at different depths) and seasonal variations on a multi-year basis. The results strengthen the view of a major role of PPP in the pelagic food web of large tropical Lake Tanganyika.