1. Abundance and bacterial production (BP) of heterotrophic bacteria (HBact) were measured in the north and south basins of Lake Tanganyika, East Africa, during seasonal sampling series between 2002 and 2007. The major objective of the study was to assess whether BP can supplement phytoplankton particulate primary production (particulate PP) in the pelagic waters, and whether BP and particulate PP are related in this large lake. HBact were enumerated in the 0-100 m surface layer by epifluorescence microscopy and flow cytometry; BP was quantified using H-thymidine incorporation, usually in three mixolimnion layers (0-40, 40-60 and 60-100 m). 2. Flow cytometry allowed three subpopulations to be distinguished: low nucleic acid content bacteria (LNA), high nucleic acid content bacteria (HNA) and Synechococcus-like picocyanobacteria (PCya). The proportion of HNA was on average 67% of total bacterial abundance, and tended to increase with depth. HBact abundance was between 1.2 × 10 and 4.8 × 10 cells mL, and was maximal in the 0-40 m layer (i.e. roughly, the euphotic layer). Using a single conversion factor of 15 fg C cell, estimated from biovolume measurements, average HBact biomass (integrated over a 100-m water column depth) was 1.89 ± 1.05 g C m . 3. Significant differences in BP appeared between seasons, especially in the south basin. The range of BP integrated over the 0-100 m layer was 93-735 mg C m day, and overlapped with the range of particulate PP (150-1687 mg C m day) measured in the same period of time at the same sites. 4. Depth-integrated BP was significantly correlated to particulate PP and chlorophyll-a, and BP in the euphotic layer was on average 25% of PP. 5. These results suggest that HBact contribute substantially to the particulate organic carbon available to consumers in Lake Tanganyika, and that BP may be sustained by phytoplankton-derived organic carbon in the pelagic waters.