The phylogenetic composition of bacterioplankton communities in Lake Tanganyika was studied by sequencing 16S rRNA gene clones. Four clone libraries were constructed from oxic epilimnion and anoxic hypolimnion samples collected during the dry season of 2002 in the northern and southern basins. Clone library analysis revealed a bacterial community composition (BCC) differing from previously studied freshwater systems and clear differences between both epi- and hypolimnion and the northern and southern basins. We detected few representatives of the Actinobacteria, Bacteroidetes, Cyanobacteria, and Alpha- and Betaproteobacteria commonly found in freshwater environments in temperate and cold regions, but observed a remarkably high number of clones belonging to Chloroflexi and Gammaproteobacteria. This was especially the case in the hypolimmon, but also in the epilimnion in the south of the lake, which suggests that the BCC may be influenced by seasonal upwelling. In total, nearly half of the detected operational taxonomical units were not closely related to bacteria previously observed in freshwater environments. Even in the epilimnetic clone libraries, genotypes commonly reported from oxic freshwater environments (e.g. ACK4, LD12, Sta2-30) were rare or absent.