Phytoplankton biomass and primary production in tropical large lakes vary at different time scales, from seasons to centuries. We provide a dataset made of 7 consecutive years of phytoplankton biomass and production in Lake Kivu (Eastern Africa). From 2002 to 2008, bi-weekly samplings were performed in a pelagic site in order to quantify phytoplankton composition and biomass, using marker pigments determined by HPLC. Primary production rates were estimated by 96 in situ (14)C incubations. A principal component analysis showed that the main environmental gradient was linked to a seasonal variation of the phytoplankton assemblage, with a clear separation between diatoms during the dry season and cyanobacteria during the rainy season. A rather wide range of the maximum specific photosynthetic rate (PBm) was found, ranging between 1.15 and 7.21gcarbong(-1)chlorophyll ah(-1), and was best predicted by a regression model using phytoplankton composition as an explanatory variable. The irradiance at the onset of light saturation (Ik) ranged between 91 and 752μEm(-2)s(-1) and was linearly correlated with the mean irradiance in the mixed layer. The inter-annual variability of phytoplankton biomass and production was high, ranging from 53 to 100mgchlorophyll am(-2) (annual mean) and from 143 to 278gcarbonm(-2)y(-1), respectively. The degree of seasonal mixing determined annual production, demonstrating the sensitivity of tropical lakes to climate variability. A review of primary production of other African great lakes allows situating Lake Kivu productivity in the same range as that of lakes Tanganyika and Malawi, even if mean phytoplankton biomass was higher in Lake Kivu.