With a volcanic origin, Lake Kivu is deep and meromictic, and shows a very particular limnology and some astonishing features. The data available on its limnology and phytoplanktic communities are limited, dispersed or outdated. This is the first deep, long term study (2002-2004) on limnology and phytoplankton ecology of Lake Kivu, combining different techniques: HPLC analysis of marker pigments, flow cytometry, light, epifluorescence and electron microscopy. Lake Kivu combines a relatively shallow euphotic layer (~18m) usually smaller than its mixed layer (20 – 60 m), and with a weak thermal gradient in the mixolimnion. With an annual average chlorophyll a in the mixed layer of 2.2 mg m-3 and low nutrient levels in the euphotic zone, the lake is clearly oligotrophic. Concerning its phytoplanktonic composition, the most common species were the pennate diatoms Nitzschia bacata Hust. and Fragilaria danica (Kütz.) Lange Bert., and the cyanobacteria Planktolyngbya limnetica (Lemm.) Komárková-Legnerová and Cronberg and Synechococcus sp. Diatoms were the dominant group in the lake, particularly during the dry season episodes of deep mixing. During the rainy season, the stratified water column, with high light and lower nutrient availability, favoured dominance of cyanobacteria. Phycoerythrin-rich phototrophic picoplankton and heterotrophic bacteria cell numbers were constantly high, with relatively subtle spatial, seasonal and vertical variations. In open lake waters, where allochthonous carbon inputs are most probably inconsequential, HNA heterotrophic bacteria abundance is strongly correlated with chlorophyll a. Recent investigations revealed an increasing methane production in the deep waters during the past three decades, leading to an accumulation of gas and the subsequent lowering of the energy required to trigger a devastating release of gasses. The role of primary producers and the probable changes on the export ratio of the organic matter into deep waters after the introduction of the planktivorous sardine from Lake Tanganyika Limnothrissa miodon, is discussed. The actual primary production, 0.71 g C m-2 d-1 (~ 260 g C m-2 y-1), doesn’t seem substantially different from some punctual measurements made in the past, which discards the hypothesis of anthropogenic eutrophication. We believe that the export ratio of organic matter into the deep waters was largely affected by biological changes that could explain part of the methane increase in the past 30 years in Lake Kivu.