Lake Kivu is a meromictic lake in East Africa with enormous amounts of dissolved methane (CH4) and carbon dioxide (CO2) in its deep waters and surprisingly low CH4 in the surface waters. We applied 454 pyrosequencing of 16S rRNA gene fragments to study the bacterial and archaeal community compositions (BCC and ACC, respectively) to provide insight into the ecology of the microbes in Lake Kivu. The vertical distribution of electron donors and acceptors in the chemically stratified water column may be responsible for the stratified distribution of microbial populations, suggesting well-defined functional specialization. The highest microbial richness was detected in the anoxic zone, which hosted high percentages of bacterial sequences related to uncultured and poorly described phyla. This suggests an under-representation of anoxic environments in current databases and the presence of previously undescribed taxa. Microbial diversity is made up of 2 fractions: abundant species (e.g. Galand et al. 2009) and rare species. Abundant species were more stable than rare species over time. The detection of rare candidate divisions (e.g. OP3, WS3, GN02) co-occurring with sulphur-oxidising Epsilonproteobacteria, sulphate- reducing Deltaproteobacteria, hydrogen-oxidising Dehalococcoidetes and methanogens might indicate interactions in the carbon and sulphur cycles in the anoxic waters.