This article reports a 3-year (2002-04) survey on limnology and phytoplankton of Lake Kivu, a meromictic lake of the East African Rift, with peculiar geophysical and geochemical features. The phytoplankton survey combined high-performance liquid chromatography (HPLC) analysis of marker pigments, flow cytometry and epifluorescence and electron microscopy. Availability of similar data from a parallel study on Lake Tanganyika allowed a detailed comparison of phytoplankton composition and ecology in these two lakes. Lake Kivu combines a relatively shallow euphotic layer, usually smaller than its mixed layer, with relatively low nutrient content of the mixolimnion and with unstable thermal stratification of the surface waters. With an annual average chlorophyll a (Chl a) in the mixed layer of 2.2 mg m and low nutrient levels in the euphotic zone, the lake is clearly oligotrophic. As in other large African Rift lakes, seasonal variations of algal biomass and composition occurred, with substantial interannual variations, mainly related to variability of wind pattern and water column stability. Contrary to earlier reports that described Lake Kivu phytoplankton as dominated by cyanobacteria and green algae, we found that diatoms were the dominant group in the lake, particularly during the dry season (DS) episodes of deep mixing. During the rainy season (RS), the stratified water column, with high light and lower nutrient availability, favoured dominance of filamentous, of diazotrophic cyanobacteria and of picocyanobacteria, which represented a substantial fraction of autotrophic biomass. Different phytoplankton functional groups were identified in Lake Kivu, which place it in an intermediate position between the oligotrophic lakes Tanganyika and Malawi and the more eutrophic Lake Victoria. However, the dominant diatoms of Lake Kivu (Urosolenia sp. and the needle-like Nitzschia bacata Hust. and Fragilaria danica Lange-Bert.) are known from oligotrophic, P-deficient African lakes, and do not seem to be adequately included in the current functional classifications of freshwater phytoplankton.